https://bioinformaticsonline.com/snippets?offset=200 https://bioinformaticsonline.com/snippets/view/42542/trimmomatic-command Tue, 05 Jan 2021 02:16:26 -0600 https://bioinformaticsonline.com/snippets/view/42542/trimmomatic-command (JitMetaENV) ➜ fastQC_out trimmomatic SE -phred33 SRR5322499_1.fastq out.trimmed.fastq LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36 TrimmomaticSE: Started with arguments: -phred33 SRR5322499_1.fastq out.trimmed.fastq LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36 Automatically using 1 threads Input Reads: 72875 Surviving: 72865 (99.99%) Dropped: 10 (0.01%) TrimmomaticSE: Completed successfully]]> Jit https://bioinformaticsonline.com/snippets/view/42541/install-trimmomatic-using-conda Tue, 05 Jan 2021 02:01:05 -0600 https://bioinformaticsonline.com/snippets/view/42541/install-trimmomatic-using-conda (JitMetaENV) ➜ fastQC_out conda install -c bioconda trimmomatic Collecting package metadata (current_repodata.json): done Solving environment: done ==> WARNING: A newer version of conda exists. <== current version: 4.9.0 latest version: 4.9.2 Please update conda by running $ conda update -n base -c defaults conda ## Package Plan ## environment location: /home/urbe/anaconda3/envs/JitMetaENV added / updated specs: - trimmomatic The following NEW packages will be INSTALLED: trimmomatic bioconda/noarch::trimmomatic-0.39-1 Proceed ([y]/n)?]]> Jit https://bioinformaticsonline.com/snippets/view/42540/install-fastqc-using-conda Tue, 05 Jan 2021 01:35:19 -0600 https://bioinformaticsonline.com/snippets/view/42540/install-fastqc-using-conda (JitMetaENV) ➜ JitMeta conda install -c bioconda fastqc Collecting package metadata (current_repodata.json): done Solving environment: done ==> WARNING: A newer version of conda exists. <== current version: 4.9.0 latest version: 4.9.2 Please update conda by running $ conda update -n base -c defaults conda ## Package Plan ## environment location: /home/urbe/anaconda3/envs/JitMetaENV added / updated specs: - fastqc The following packages will be downloaded: package | build ---------------------------|----------------- fastqc-0.11.9 | 0 9.7 MB bioconda font-ttf-dejavu-sans-mono-2.37| hab24e00_0 388 KB conda-forge fontconfig-2.13.1 | h736d332_1003 319 KB conda-forge freetype-2.10.4 | h7ca028e_0 912 KB conda-forge libpng-1.6.37 | h21135ba_2 306 KB conda-forge libuuid-2.32.1 | h7f98852_1000 28 KB conda-forge openjdk-10.0.2 | h14c3975_1015 189.2 MB conda-forge ------------------------------------------------------------ Total: 200.8 MB The following NEW packages will be INSTALLED: fastqc bioconda/noarch::fastqc-0.11.9-0 font-ttf-dejavu-s~ conda-forge/noarch::font-ttf-dejavu-sans-mono-2.37-hab24e00_0 fontconfig conda-forge/linux-64::fontconfig-2.13.1-h736d332_1003 freetype conda-forge/linux-64::freetype-2.10.4-h7ca028e_0 libpng conda-forge/linux-64::libpng-1.6.37-h21135ba_2 libuuid conda-forge/linux-64::libuuid-2.32.1-h7f98852_1000 openjdk conda-forge/linux-64::openjdk-10.0.2-h14c3975_1015 Proceed ([y]/n)?]]> Jit https://bioinformaticsonline.com/snippets/view/42538/install-grabseqs-with-conda Mon, 04 Jan 2021 11:20:47 -0600 https://bioinformaticsonline.com/snippets/view/42538/install-grabseqs-with-conda (JitMetaENV) ➜ JitMeta conda install grabseqs -c louiejtaylor -c bioconda -c conda-forge Collecting package metadata (current_repodata.json): done Solving environment: done ==> WARNING: A newer version of conda exists. <== current version: 4.9.0 latest version: 4.9.2 Please update conda by running $ conda update -n base -c defaults conda ## Package Plan ## environment location: /home/urbe/anaconda3/envs/JitMetaENV added / updated specs: - grabseqs The following packages will be downloaded: package | build ---------------------------|----------------- argparse-1.4.0 | py36_0 46 KB bioconda c-ares-1.11.0 | h470a237_1 87 KB bioconda ca-certificates-2020.12.5 | ha878542_0 137 KB conda-forge certifi-2020.12.5 | py36h5fab9bb_0 143 KB conda-forge curl-7.71.1 | he644dc0_8 139 KB conda-forge gettext-0.19.8.1 | h0b5b191_1005 3.6 MB conda-forge grabseqs-0.5.0 | py36_0 35.7 MB louiejtaylor hdf5-1.10.5 |nompi_h5b725eb_1113 3.1 MB conda-forge icu-68.1 | h58526e2_0 13.0 MB conda-forge krb5-1.17.2 | h926e7f8_0 1.4 MB conda-forge ld_impl_linux-64-2.35.1 | hea4e1c9_1 617 KB conda-forge libcurl-7.71.1 | hcdd3856_8 312 KB conda-forge libedit-3.1.20191231 | he28a2e2_2 121 KB conda-forge libev-4.33 | h516909a_1 104 KB conda-forge libffi-3.3 | h58526e2_2 51 KB conda-forge libgfortran-ng-9.3.0 | he4bcb1c_17 22 KB conda-forge libgfortran5-9.3.0 | he4bcb1c_17 2.0 MB conda-forge libidn2-2.3.0 | h516909a_0 97 KB conda-forge libnghttp2-1.41.0 | hab1572f_1 709 KB conda-forge libssh2-1.9.0 | hab1572f_5 225 KB conda-forge libunistring-0.9.10 | h14c3975_0 1.4 MB conda-forge libxml2-2.9.10 | h72842e0_3 1.3 MB conda-forge ncbi-ngs-sdk-2.10.9 | h3e72335_0 141 KB bioconda ncurses-6.2 | h58526e2_4 985 KB conda-forge openssl-1.1.1i | h7f98852_0 2.1 MB conda-forge ossuuid-1.6.2 | hf484d3e_1000 56 KB conda-forge perl-5.26.2 | h36c2ea0_1008 15.4 MB conda-forge perl-app-cpanminus-1.7044 | pl526_1 234 KB bioconda perl-business-isbn-3.004 | pl526_0 15 KB bioconda perl-business-isbn-data-20140910.003| pl526_0 15 KB bioconda perl-carp-1.38 | pl526_3 15 KB bioconda perl-constant-1.33 | pl526_1 10 KB bioconda perl-data-dumper-2.173 | pl526_0 35 KB bioconda perl-encode-2.88 | pl526_1 2.1 MB bioconda perl-exporter-5.72 | pl526_1 13 KB bioconda perl-extutils-makemaker-7.36| pl526_1 153 KB bioconda perl-file-path-2.16 | pl526_0 17 KB bioconda perl-file-temp-0.2304 | pl526_2 26 KB bioconda perl-mime-base64-3.15 | pl526_1 15 KB bioconda perl-parent-0.236 | pl526_1 5 KB bioconda perl-uri-1.76 | pl526_0 55 KB bioconda perl-xml-libxml-2.0132 | pl526h7ec2d77_1 260 KB bioconda perl-xml-namespacesupport-1.12| pl526_0 11 KB bioconda perl-xml-sax-1.02 | pl526_0 36 KB bioconda perl-xml-sax-base-1.09 | pl526_0 19 KB bioconda perl-xsloader-0.24 | pl526_0 8 KB bioconda pigz-2.3.4 | hed695b0_1 76 KB conda-forge pip-20.3.3 | pyhd8ed1ab_0 1.1 MB conda-forge python-3.6.12 |hffdb5ce_0_cpython 38.4 MB conda-forge requests-2.12.5 | py36_0 771 KB conda-forge sqlite-3.34.0 | h74cdb3f_0 1.4 MB conda-forge sra-tools-2.10.9 | pl526haddd2b5_0 61.9 MB bioconda tk-8.6.10 | h21135ba_1 3.2 MB conda-forge wget-1.20.1 | h22169c7_0 788 KB conda-forge wheel-0.36.2 | pyhd3deb0d_0 31 KB conda-forge ------------------------------------------------------------ Total: 193.7 MB The following NEW packages will be INSTALLED: _libgcc_mutex conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge _openmp_mutex conda-forge/linux-64::_openmp_mutex-4.5-1_gnu argparse bioconda/linux-64::argparse-1.4.0-py36_0 c-ares bioconda/linux-64::c-ares-1.11.0-h470a237_1 ca-certificates conda-forge/linux-64::ca-certificates-2020.12.5-ha878542_0 certifi conda-forge/linux-64::certifi-2020.12.5-py36h5fab9bb_0 curl conda-forge/linux-64::curl-7.71.1-he644dc0_8 gettext conda-forge/linux-64::gettext-0.19.8.1-h0b5b191_1005 grabseqs louiejtaylor/linux-64::grabseqs-0.5.0-py36_0 hdf5 conda-forge/linux-64::hdf5-1.10.5-nompi_h5b725eb_1113 icu conda-forge/linux-64::icu-68.1-h58526e2_0 krb5 conda-forge/linux-64::krb5-1.17.2-h926e7f8_0 ld_impl_linux-64 conda-forge/linux-64::ld_impl_linux-64-2.35.1-hea4e1c9_1 libcurl conda-forge/linux-64::libcurl-7.71.1-hcdd3856_8 libedit conda-forge/linux-64::libedit-3.1.20191231-he28a2e2_2 libev conda-forge/linux-64::libev-4.33-h516909a_1 libffi conda-forge/linux-64::libffi-3.3-h58526e2_2 libgcc-ng conda-forge/linux-64::libgcc-ng-9.3.0-h5dbcf3e_17 libgfortran-ng conda-forge/linux-64::libgfortran-ng-9.3.0-he4bcb1c_17 libgfortran5 conda-forge/linux-64::libgfortran5-9.3.0-he4bcb1c_17 libgomp conda-forge/linux-64::libgomp-9.3.0-h5dbcf3e_17 libiconv conda-forge/linux-64::libiconv-1.16-h516909a_0 libidn2 conda-forge/linux-64::libidn2-2.3.0-h516909a_0 libnghttp2 conda-forge/linux-64::libnghttp2-1.41.0-hab1572f_1 libssh2 conda-forge/linux-64::libssh2-1.9.0-hab1572f_5 libstdcxx-ng conda-forge/linux-64::libstdcxx-ng-9.3.0-h2ae2ef3_17 libunistring conda-forge/linux-64::libunistring-0.9.10-h14c3975_0 libxml2 conda-forge/linux-64::libxml2-2.9.10-h72842e0_3 ncbi-ngs-sdk bioconda/linux-64::ncbi-ngs-sdk-2.10.9-h3e72335_0 ncurses conda-forge/linux-64::ncurses-6.2-h58526e2_4 openssl conda-forge/linux-64::openssl-1.1.1i-h7f98852_0 ossuuid conda-forge/linux-64::ossuuid-1.6.2-hf484d3e_1000 perl conda-forge/linux-64::perl-5.26.2-h36c2ea0_1008 perl-app-cpanminus bioconda/linux-64::perl-app-cpanminus-1.7044-pl526_1 perl-business-isbn bioconda/linux-64::perl-business-isbn-3.004-pl526_0 perl-business-isb~ bioconda/linux-64::perl-business-isbn-data-20140910.003-pl526_0 perl-carp bioconda/linux-64::perl-carp-1.38-pl526_3 perl-constant bioconda/linux-64::perl-constant-1.33-pl526_1 perl-data-dumper bioconda/linux-64::perl-data-dumper-2.173-pl526_0 perl-encode bioconda/linux-64::perl-encode-2.88-pl526_1 perl-exporter bioconda/linux-64::perl-exporter-5.72-pl526_1 perl-extutils-mak~ bioconda/linux-64::perl-extutils-makemaker-7.36-pl526_1 perl-file-path bioconda/linux-64::perl-file-path-2.16-pl526_0 perl-file-temp bioconda/linux-64::perl-file-temp-0.2304-pl526_2 perl-mime-base64 bioconda/linux-64::perl-mime-base64-3.15-pl526_1 perl-parent bioconda/linux-64::perl-parent-0.236-pl526_1 perl-uri bioconda/linux-64::perl-uri-1.76-pl526_0 perl-xml-libxml bioconda/linux-64::perl-xml-libxml-2.0132-pl526h7ec2d77_1 perl-xml-namespac~ bioconda/linux-64::perl-xml-namespacesupport-1.12-pl526_0 perl-xml-sax bioconda/noarch::perl-xml-sax-1.02-pl526_0 perl-xml-sax-base bioconda/linux-64::perl-xml-sax-base-1.09-pl526_0 perl-xsloader bioconda/linux-64::perl-xsloader-0.24-pl526_0 pigz conda-forge/linux-64::pigz-2.3.4-hed695b0_1 pip conda-forge/noarch::pip-20.3.3-pyhd8ed1ab_0 python conda-forge/linux-64::python-3.6.12-hffdb5ce_0_cpython python_abi conda-forge/linux-64::python_abi-3.6-1_cp36m readline conda-forge/linux-64::readline-8.0-he28a2e2_2 requests conda-forge/linux-64::requests-2.12.5-py36_0 setuptools conda-forge/linux-64::setuptools-49.6.0-py36h9880bd3_2 sqlite conda-forge/linux-64::sqlite-3.34.0-h74cdb3f_0 sra-tools bioconda/linux-64::sra-tools-2.10.9-pl526haddd2b5_0 tk conda-forge/linux-64::tk-8.6.10-h21135ba_1 wget conda-forge/linux-64::wget-1.20.1-h22169c7_0 wheel conda-forge/noarch::wheel-0.36.2-pyhd3deb0d_0 xz conda-forge/linux-64::xz-5.2.5-h516909a_1 zlib conda-forge/linux-64::zlib-1.2.11-h516909a_1010 Proceed ([y]/n)?]]> Jit https://bioinformaticsonline.com/snippets/view/42537/create-a-conda-environment Mon, 04 Jan 2021 11:18:08 -0600 https://bioinformaticsonline.com/snippets/view/42537/create-a-conda-environment JitMeta (base) ➜ JitMeta conda create --name JitMetaENV Collecting package metadata (current_repodata.json): done Solving environment: done ==> WARNING: A newer version of conda exists. <== current version: 4.9.0 latest version: 4.9.2 Please update conda by running $ conda update -n base -c defaults conda ## Package Plan ## environment location: /home/urbe/anaconda3/envs/JitMetaENV Proceed ([y]/n)? y Preparing transaction: done Verifying transaction: done Executing transaction: done # # To activate this environment, use # # $ conda activate JitMetaENV # # To deactivate an active environment, use # # $ conda deactivate]]> Jit https://bioinformaticsonline.com/snippets/view/42409/install-sibeliaz-in-your-linux-cluster Sun, 20 Dec 2020 00:40:32 -0600 https://bioinformaticsonline.com/snippets/view/42409/install-sibeliaz-in-your-linux-cluster (jitenv) jitendra@Bathymodiolus:~$ conda install -c bioconda sibeliaz Collecting package metadata (current_repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source. Collecting package metadata (repodata.json): done Solving environment: done ## Package Plan ## environment location: /home/jitendra/.conda/envs/jitenv added / updated specs: - sibeliaz The following packages will be downloaded: package | build ---------------------------|----------------- _anaconda_depends-2019.10 | py27_0 6 KB anaconda-custom | py27_1 3 KB ca-certificates-2020.12.8 | h06a4308_0 121 KB certifi-2020.6.20 | pyhd3eb1b0_3 155 KB maf2synteny-1.0 | he1b5a44_0 61 KB bioconda openssl-1.1.1i | h27cfd23_0 2.5 MB sibeliaz-1.2.2 | he1b5a44_0 101 KB bioconda spoa-4.0.3 | he513fc3_0 103 KB bioconda tbb-2020.3 | hfd86e86_0 1.1 MB twopaco-0.9.4 | he1b5a44_0 374 KB bioconda ------------------------------------------------------------ Total: 4.5 MB The following NEW packages will be INSTALLED: _anaconda_depends pkgs/main/linux-64::_anaconda_depends-2019.10-py27_0 maf2synteny bioconda/linux-64::maf2synteny-1.0-he1b5a44_0 sibeliaz bioconda/linux-64::sibeliaz-1.2.2-he1b5a44_0 spoa bioconda/linux-64::spoa-4.0.3-he513fc3_0 twopaco bioconda/linux-64::twopaco-0.9.4-he1b5a44_0 The following packages will be UPDATED: ca-certificates 2019.8.28-0 --> 2020.12.8-h06a4308_0 certifi pkgs/main/linux-64::certifi-2019.9.11~ --> pkgs/main/noarch::certifi-2020.6.20-pyhd3eb1b0_3 openssl 1.1.1d-h7b6447c_2 --> 1.1.1i-h27cfd23_0 tbb 2019.4-hfd86e86_0 --> 2020.3-hfd86e86_0 The following packages will be DOWNGRADED: anaconda 2019.10-py27_0 --> custom-py27_1 Proceed ([y]/n)? y Downloading and Extracting Packages sibeliaz-1.2.2 | 101 KB | ######################################################################## | 100% maf2synteny-1.0 | 61 KB | ######################################################################## | 100% certifi-2020.6.20 | 155 KB | ######################################################################## | 100% spoa-4.0.3 | 103 KB | ######################################################################## | 100% ca-certificates-2020 | 121 KB | ######################################################################## | 100% openssl-1.1.1i | 2.5 MB | ######################################################################## | 100% anaconda-custom | 3 KB | ######################################################################## | 100% _anaconda_depends-20 | 6 KB | ######################################################################## | 100% twopaco-0.9.4 | 374 KB | ######################################################################## | 100% tbb-2020.3 | 1.1 MB | ######################################################################## | 100% Preparing transaction: done Verifying transaction: done Executing transaction: done (jitenv) jitendra@Bathymodiolus:~$ sibeliaz You must provide the input file name (jitenv) jitendra@Bathymodiolus:~$ sibeliaz -h Usage: [-k <odd integer>] [-b <integer>] [-m <integer>] [-a <integer>] [-t <integer>] [-f <integer>] [-o <output_directory>] [-n] <input file> (jitenv) jitendra@Bathymodiolus:~$]]> Jit https://bioinformaticsonline.com/snippets/view/42284/print-the-screenshot-of-read-coverage-remotely Fri, 30 Oct 2020 01:07:04 -0500 https://bioinformaticsonline.com/snippets/view/42284/print-the-screenshot-of-read-coverage-remotely #Chrom_2:9700000-9760000 ASCIIGenome -ni --fasta A_vaga.NDPD.fasta -r Chrom_2:9700000-9760000 -x "save >> test.pdf" A_vaga.NDPD.fasta.out.sam.bam.sorted.bam]]> Jit https://bioinformaticsonline.com/snippets/view/42193/picard-tools-command-to-get-some-insert-statistics Sun, 06 Sep 2020 10:23:15 -0500 https://bioinformaticsonline.com/snippets/view/42193/picard-tools-command-to-get-some-insert-statistics #picard tools to get some insert statistics to see whether our reads seem to be in the correct place #module load picard/2.0.1 java -Xmx16g -XX:PermSize=8g -jar $PICARD_HOME/picard.jar CollectInsertSizeMetrics MINIMUM_PCT=0 HISTOGRAM_FILE=<assembly name>.pdf INPUT=<sorted-bam-filename> OUTPUT=<assembly name>.sorted.collectInseSize HISTOGRAM_WIDTH=500]]> Neel https://bioinformaticsonline.com/snippets/view/42186/concatenate-two-given-sequences-and-find-the-length-of-the-new-sequence-and-also-print-out-the-second-codon-of-the-sequence Thu, 03 Sep 2020 06:47:43 -0500 https://bioinformaticsonline.com/snippets/view/42186/concatenate-two-given-sequences-and-find-the-length-of-the-new-sequence-and-also-print-out-the-second-codon-of-the-sequence #!/usr/bin/perl use strict; use warnings; #assign strings to variables my $DNA = "GATTACACAT"; my $polyA = "AAAA"; #concatenate two strings my $modifiedDNA = $DNA.$polyA; #calculate the length of $modifiedDNA and #print out the value of the variable and its length my $DNAlength = length($modifiedDNA); print "Modified DNA: $modifiedDNA has length $DNAlength\n"; #extract the second codon in $modifiedDNA my $codon = substr($modifiedDNA,3,3); print "Second codon is $codon\n";]]> Nishi Singh https://bioinformaticsonline.com/snippets/view/42134/bash-script-to-handle-multifasta-files Mon, 17 Aug 2020 05:32:14 -0500 https://bioinformaticsonline.com/snippets/view/42134/bash-script-to-handle-multifasta-files #Convert all lowercase residues to uppercase in a FASTA sequence file $ awk 'BEGIN{FS=" "}{if(!/>/){print toupper($0)}else{print $1}}' input.fasta > output.fasta #Rearrange FASTA sequences according to their length $ awk '/^>/ {printf("%s%s\t",(N>0?"\n":""), $0);N++;next;} {printf("%s",$0);} END {printf("\n");}' input.fasta |\ >awk -F '\t' '{printf("%d\t%s\n",length($2),$0;)}' |\ >sort -k1,1n | cut -f 2- |tr "\t" "\n" > output.fasta #Add ‘>’ at the beginning of headers in a FASTA file $ awk '{if ($0 ~/_/) {printf ">";} print $0; }' input.fasta > output.fasta #Match FASTA headers in two different multi-FASTA files $ awk 'NR=FNR{a[$0];next}$0 in a{print $0}' input1.fasta input2.fasta #Merge all FASTA files in a directory into a single FASTA file $ awk'1' *.fa > all.fa]]> BioStar