Results for "group"
Bio-Scripts
Perl script to find coding regions in DNA sequences
...# extract the two values or columns with a regular expression # A group of letters and a decimal numb...a regular expression will be used searching for all of the # possible groups of three symbols (option g)...2170 days ago
- ...tId Maximum spot id --spot-groups Filter by SPOT_GROUP (member): name[,...] -W|-...eads and above are ignored. -G|--spot-group Split into f...name, $sg spot group (barcode), $sl spot...
2141 days ago
- ...m cross-sample contamination CalculateReadGroupChecksum (Picard) Creates a hash code based on the read groups (RG). CheckFingerprin...qualities and adds the mate cigar tag to read-group BAMs RevertSam (Picard)...
2090 days ago
Bash script to alignment of short reads against reference genome !
...#alignment with bwa: bwa mem -t $threads -R '@RG\tID:K12\tSM:K12' --- this says "align using so many threads" and also "give the reads the read group K12 and the sample name K12"...1574 days ago
To convert just one specific read group to fastq
...ard FastqToSam F1=reads/{}_1.fastq F2=reads/{}_1.fastq O=bam/{}.bam RG=GROUP-{} LB=LIB-{} SM=SAMPLE_{} QUI...into one. samtools merge -f all.bam bam/*.bam # Investigate the readgroups in the header. echo "" ech...1557 days ago
Installing docker for Bioinformatics on Ubuntu !
...on-root user, you should now consider adding your user to the "docker" group with something like: sud...k in for this to take effect! WARNING: Adding a user to the "docker" group will grant the ability to run...1528 days ago
Pack a perl program with their dependencies on Ubuntu !
...ResearchLabsQuestionsPagesDiscussionMoreBioScriptsBlogsBookmarksFilesFunGroupsPollsThe WireTrystVideos...l genomes, enabling new insights into evolution and sequence... Latest groups Bioinformatics related com...1526 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.fas904 days ago
