Results for "Group Research"
Bio-Scripts
Perl script to find coding regions in DNA sequences
#!/usr/bin/perl -w use strict; # if the number of input arguments is lower than...o values or columns with a regular expression # A group of letters and a decimal numb...n will be used searching for all of the # possible groups o...2150 days ago
- ➜ bin git:(master) ✗ ./fastq-dump --help Usage: ./fastq-dump [...Maximum spot id --spot-groups Filter by SPOT_GROUP (member): name[,...] -W|-...above are ignored. -G|--spot-group Split into f...name, $sg spot group (b...
2122 days ago
- jitendra@jitendra-UNLOCK-INSTALL[SNP] wget https://github.com/broadinstit...ample contamination CalculateReadGroupChecksum (Picard) Creates a hash code based on the read groups (RG). CheckFingerprin...s and adds the mate cigar tag to read-group BA...
2071 days ago
Installing pb-assembly on Linux !
[jnarayan@hmem00 ~]$ module avail ------------------...ot # # necessarily ISO compliant, intended for Research Use Only and not for use #...ot # # necessarily ISO compliant, intended for Research Use Only and not for use #...2030 days ago
Setting up falconUnzip conda environments for genome assembly !
➜ Analysis_Results conda create -n denovo_asm Solving...ot # # necessarily ISO compliant, intended for Research Use Only and not for use #...ot # # necessarily ISO compliant, intended for Research Use Only and not for use #...1985 days ago
Bash script to alignment of short reads against reference genome !
bwa mem -t 40 -R '@RG\tID:K12\tSM:K12' \ E.coli_K12_MG1655.fa SRR1770413_1.fastq.gz SRR1770413_2.fastq.gz \...--- this says "align using so many threads" and also "give the reads the read group K1...1554 days ago
To convert just one specific read group to fastq
# Stop script on error. set -uex # The SRR BioProject number for the sequencing dat...ads/{}_1.fastq F2=reads/{}_1.fastq O=bam/{}.bam RG=GROUP-{} LB=LIB-{} SM=SAMPLE_{} QUI...merge -f all.bam bam/*.bam # Investigate the readgroups i...1538 days ago
Installing docker for Bioinformatics on Ubuntu !
jit@jit-HP-Pro-3335-MT:~/Downloads$ sudo apt-get remove docker docker-engine docker.io...ould now consider adding your user to the "docker" group with something like: sud...e effect! WARNING: Adding a user to the "docker" group wi...1509 days ago
Pack a perl program with their dependencies on Ubuntu !
...ActivityNewsOpportunityResearchLabsQuestionsPagesDiscussio...reBioScriptsBlogsBookmarksFilesFunGroupsPollsThe WireTrystVideos...evolution and sequence... Latest groups Bioinformatics related compan...ear to share a core set of genes. Researchers have also found that two-t...1507 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.fas885 days ago
