Results for "The winner of the Sanger Institute Prize will be offered a three-month internship with a research group at the Wellcome Sanger Institute"
Bio-Scripts
Perl script to find coding regions in DNA sequences
...2 # return a message showing the error if (scalar(@ARGV) < 2...act the two values or columns with a regular expression # A group of letters and a decimal numb...+) (\d+\.\d+)/); # load the hash table $pcodons{$codon}...input DNA sequence. To split the sequence in segments of lengt...2161 days ago
- ...Maximum spot id --spot-groups Filter by SPOT_GROUP (mem...set, otherwise - to individual reads...either be accession.version (ex:...dual reads Applied only with --split-spot set --skip-tec...
2132 days ago
- jitendra@jitendra-UNLOCK-INSTALL[SNP] wget https://github.com/broadinstitute/gatk/releases/download/...age template for Spark tools (will NOT work on non-Spark tools)...: LOCAL: run using the in-mem...GVCF files into a single GVCF with appropriate annotations Genom...
2081 days ago
Installing pb-assembly on Linux !
[jnarayan@hmem00 ~]$ module avail --------------------------...es found; did you mean one of these? libgcc-ng: libgcc...The following NEW packages will be INSTALLED: bwa: 0...The following NEW packages will be INSTALLED: bzip2:...y ISO compliant, intended for Resea...2040 days ago
Setting up falconUnzip conda environments for genome assembly !
...ecs: - pb-assembly The following packages will be downloaded: package...# # possibly newer than the currently available SMRT(R) Analys...warranty that any such issue will be addressed, # # to any extent or within any time frame....1996 days ago
Bash script to alignment of short reads against reference genome !
bwa mem -t 40 -R '@RG\tID:K12\tSM:K12' \...king it down by line: #alignment with bwa: b...ing so many threads" and also "give the reads the read group K12 and the sample name K12...stdin (the - specifier in place of the fi...is that we'll tell it we're working with shor...1565 days ago
To convert just one specific read group to fastq
# Stop script on error. set -uex # The SRR BioProject number for the sequen...nfo > runinfo.txt # Select the first N elements. Keep only v...s/{}_1.fastq O=bam/{}.bam RG=GROUP-{} LB=LIB-{} SM=SAMPLE_{} Q...e 2>> log.txt" # Merge all the BAM files into one. samtools...1548 days ago
Installing docker for Bioinformatics on Ubuntu !
jit@jit-HP-Pro-3335-MT:~/Downloads$ sudo apt-get remove docker d...consider adding your user to the "docker" group with something like: sudo use...cker jit Remember that you will have to log out and back in f...WARNING: Adding a user to the "docker" group will grant the ability to run...1519 days ago
Pack a perl program with their dependencies on Ubuntu !
...ng state information... Done The following additional packages will...par-dist-perl libpar-perl The following NEW packages will be installed: libgetopt-ar...untu0.1) ... #you can find the test script web.pl at https://...oScriptsBlogsBookmarksFilesFunGroupsPollsThe WireTrystVideos...1517 days ago
Extract fasta sequences with ids in another file !
#Ids are in test.txt - one ids per line #sequences are in test.fa grep -w -A 2 -f test.txt test.fa --no-group-separator # seqtk seqtk subseq test.fa test.txt #faSomeRecods faSomeRecords in.fa listFile out.fa # seqkit seqkit grep -n -f list.txt sequences.fas > newfile2.fas895 days ago
