Results for "Symbol IDs Convert"
Bio-Scripts
Perl script to extract sequence by Ids from multifasta file !
#!/usr/bin/perl -w use strict; my $idsfile = "$ARGV[0]"; my $seqfile = "$ARGV[1]"; my %ids = (); open FILE, $idsfile; while() { chomp; $ids{$_} += 1; } close FILE; local $/ = "\n>";...as first word in FASTA header if (exists($ids{$id...2106 days ago
- jitendra@jitendra-UNLOCK-INSTALL[SNP] wge...input ".sam" or ".bam" files. ConvertSequencingArtifactToOxoG (Pica...tervalList (Picard) Converts a BED file to a Picard Inter...nnotations to VCF files VcfFormatConverter (Picard) C...
2086 days ago
- # Convert FASTQ to FASTA seqtk seq -a IN.fastq > OUT.fasta # Convert FASTQ to FASTA and set bases of quality lower than 20 to N seqtk seq -aQ64 -q20 -n N IN.fastq > OUT.fasta # Download Seqtk https://github.com/lh3/seqtk
1736 days ago
Samtools commands for bioinformatician !
## count mapped reads samtools view -c -F 260 mapping_file.bam ### converting sam file into fasta samto...reads_mapped.sam > reads.fasta ### converting sam file into bam # -b :...######## # try these recipies: ### convert BAM to FASTA: samtools view...1613 days ago
- $ sudo apt install npm Reading package lists... Done Building...ssion-parse node-spdx-license-ids node-tar node-tunnel-agent...verse amd64 node-spdx-license-ids all 1.2.2-1 [4,792 B] Get:22...ted package node-spdx-license-ids. Preparing to unpack .../20-...Setting up node-spdx-license-ids (1....
1563 days ago
To convert just one specific read group to fastq
# Stop script on error. set -uex # The SRR BioProject number for the sequencing...roups to paired files. samtools fastq -t -1 all1.fq -2 all2.fq all.bam # To convert just one specific read group....1553 days ago
- #This method can be applied directly to FASTA or a FASTQ file, compressed or uncompressed files. Seqtk is a fast and lightweight tool for processing biological data (FA...
1413 days ago
Sequence Ids conversion files !
ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/ Name Size Date Modified ARCHIVE/ 02/01/2020, 05:30:00 ASN_BINARY/ 03/07/2020, 07:49:00 GENE_INFO/ 03/07/2020, 07:48:00 0...1413 days ago
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 #...1368 days ago
- (JitMetaENV) ➜ assembly conda install -c bioconda prokka Collecting package metadata (current_repodata.json): done Solving environment: failed with initial frozen so...
1226 days ago
