Results for "BGI Group"
Bio-Scripts
Perl script to find coding regions in DNA sequences
#!/usr/bin/perl -w use strict; # if the number...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 of three symbols (option g)...2159 days ago
- ➜ bin git:(master) ✗ ./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 (barcode), $sl spot...
2130 days ago
- jitendra@jitendra-UNLOCK-INSTALL[SNP] wget...sample contamination CalculateReadGroupChecksum (Picard) Creates a hash code based on the read groups (RG). CheckFingerprin...es and adds the mate cigar tag to read-group BAMs RevertSam (Picard)...
2079 days ago
Bash script to alignment of short reads against reference genome !
bwa mem -t 40 -R '@RG\tID:K12\tSM:K12' \ E.coli_K12_MG1655.fa SRR1770413_1.fas...' --- this says "align using so many threads" and also "give the reads the read group K12 and the sample name K12"...1563 days ago
To convert just one specific read group to fastq
# Stop script on error. set -uex # The SRR BioProje...ads/{}_1.fastq F2=reads/{}_1.fastq O=bam/{}.bam RG=GROUP-{} LB=LIB-{} SM=SAMPLE_{} QUI...merge -f all.bam bam/*.bam # Investigate the readgroups in the header. echo "" ech...1546 days ago
Installing docker for Bioinformatics on Ubuntu !
jit@jit-HP-Pro-3335-MT:~/Downloads$ sudo apt-get remove...ould now consider adding your user to the "docker" group with something like: sud...e effect! WARNING: Adding a user to the "docker" group will grant the ability to run...1517 days ago
Pack a perl program with their dependencies on Ubuntu !
#Follow steps to create your own executable ./web ji...sPagesDiscussionMoreBioScriptsBlogsBookmarksFilesFunGroupsPollsThe WireTrystVideos...new insights into evolution and sequence... Latest groups Bioinformatics related com...1515 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.fas893 days ago
