BOL: Results for "samtools"

Results for "samtools"

- Jit@jit.aber
How to install Perl modules manually, using CPAN command, and other quick ways
...un - BioPerl wrappers: scriptslibbio-perl-perl - BioPerl core perl moduleslibbio-perl-run-perl - BioPerl wrappers: moduleslibbio-samtools-perl - Perl interface to SamTools library for DNA sequencinglib...
3942 days ago
- Jit@jit.aber
Converting a VCF into a FASTA given some reference !
Samtools/BCFtools (Heng Li) provides a Perl script vcfutils.pl which does th...ithub.com/gringer/bioinfscripts/blob/master/vcf2fq.pl https://github.com/lh3/samtools/blob/master/bcftools/vcfutils...
2108 days ago
+2 more Blogs

- Jitendra Narayan@admin
List of popular bioinformatics software/tools
In current genome era, our day to day work is to handle the huge geneome sequences, expression data, several other datasets. This link provide a comprehensive list of commonly used sofware/tools.
3938 days ago
- Rahul Nayak@rahul
Bioinformatics Protocols
...al Variant Detection (Advanced) Tutorial In this tutorial we compare the performance of three statistically-based variant detection tools:* SAMtools: Mpileup* GATK: Unified Genot...
3645 days ago
+14 more Bookmarks

- Jit@jit.aber
Download blasr 1.3 version
..._open_format] Failed to open file temporarySamsamtools sort: can't open "temporarySa...ai - | grep '$^@\|XT:A:U$' | /usr/local/bin/samtools view -S -h -b -F 0x4 - | /usr...f-with-repeat.bam repeat.dat | /usr/local/bin/samtools view - -h -S -b > FALCON-U...
2144 days ago

- Rahul Agarwal@raag
Structure of Binary files used for storing sequencing data-bam and sff
...t they occupy less space in memory with maximum information content. Link for those who looking for structure of Bam and sff file: Bam: http://samtools.sourceforge.net/SAMv1.pdf&nbs...
3912 days ago
- Rahul Nayak@rahul
Useful Publications and Websites for Deep Sequencing Data Analysis
...Research 22(5): 939–946. PubMedCentral Data formats, data management, and alignment software tools The Sequence Alignment/Map format and SAMtools. Li et al, Bioinformatics 25(...
3772 days ago
+11 more Top-level pages

- Jit@jit.aber
Extract list of read ID from bam file: samtools view mbi.sorted.bam |perl -ne '/ID/ && print' > extractedID.sam #Extract #Ids #SAM #BAM #NGS
3627 days ago
- Aaryan Lokwani@aaryan
Count the contigs length in index fasta file with samtools. $ awk '{s+=$2}END{print s}' scaffolds.fasta.fai #Fasta #Index #Length #Count #Size #Samtools
2136 days ago
+14 more Wire posts

- Jit@jit.aber
BASH script for SelfBLAST a genome
#!/bin/bash #self BLAST a genome -- Expecting you have blast and samtools installed in your system #Autho...$2 for you from $FASTAFILE -- MAKE SURE U HAVE ADDED CORRECT NAME" samtools faidx MergedContigs.fasta...
2644 days ago
- Archana Malhotra@archana
Extract fasta sequence with Ids with Bash script
#!/bin/bash while IFS='' read -r line || [[ -n "$line" ]]; do echo "Text read from file: $line" samtools faidx ONT.fasta $line > $line.faa done < "$1"
2347 days ago
+26 more Bio-Scripts

- Jit@jit.aber
Comment on "Setting up autoConTAMPR !"
......Setting up phyml (2:20120412-2) ...Setting up primer3 (2.3.6-1) ...Setting up probalign (1.4-3) ...Setting up probcons (1.12-9) ...Setting up samtools (0.1.19-1) ...Setting up sim4...
1434 days ago
- Jit@jit.aber
Comment on "ASCIIGenome: genome browser based on command line interface and designed for running from console terminals."
...bsp; samtools [-f INT=0] [-F INT=4] [-q INT...sp; Apply samtools filters to alignment tracks c...
1512 days ago
+7 more Comments