Results for "bam"

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  • 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.

    Tags: Bioinformatics, SamTool, SAM, BAM, IGV, BLAT, Software, Tools

    1529 days ago

  • Extract list of read ID from bam file: samtools view mbi.sorted.bam |perl -ne '/ID/ && print' > extractedID.sam #Extract #Ids #SAM #BAM #NGS

    Tags: Extract, Ids, SAM, BAM, NGS

    1218 days ago

  • Picard

    Picard is a set of command line tools for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF. These file formats are defined in the Hts-specs repository. See especially the SAM specification and the VCF specification. Note that the information on this pag...

    Tags: Bioinformatics, NGS, Assembly, BAM, SAM, CRAM, Picard, FastQC, Tool, Software

    512 days ago

  • #BAM file to fasta #conversion with #Samtool: samtools view filename.bam | \ awk '{OFS="\t"; print ">"$1"\n"$10}' - > filename.fasta

    Tags: BAM, conversion, Samtool

    549 days ago

  • #BAM file to #fastaq #conversion with #Samtool: samtools view filename.bam | awk '{OFS="\t"; print "@"$1"\n"$10"\n+\n"$11}' >| filename.fastq

    Tags: BAM, fastaq, conversion, Samtool

    549 days ago

  • #Extract all #Reads from #BAM file for a #region Chr10:18000-45500 using #samtools: samtools view input.bam "Chr10:18000-45500" > output.bam

    Tags: Extract, Reads, BAM, region, samtools

    455 days ago

  • #Extract #tabbed info from #BAM file with samtools: samtools view test.bam|awk '{print $1 "\t" $2 "\t" $3 "\t" $4 "\t" $4+length($10)-1}' > file.xls

    Tags: Extract, tabbed, BAM

    457 days ago

  • Check if BAM file is sorted or not use: for F in `find . -name "*.bam"`; do echo $F; samtools index ${F} ; done #Sort #BAM #Trick

    Tags: Sort, BAM, Trick

    453 days ago

  • Extract reference nucleotide from BAM file: samtools view your.bam | awk '{print substr( $10, 100, 1)}' #SAM #BAM #Samtools #Tricks #NGS

    Tags: SAM, BAM, Samtools, Tricks, NGS

    450 days ago

  • Fancy Oneliner for Bioinformatics !!

    This webpage lists some of the one-liners that we frequently use in metagenomic analyses. You can click on the following links to browse through different topics. You can copy/paste the commands as they are in your terminal screen, provided you follow the same naming conventions and folder struct...

    Tags: Bioinformatics, Analysis, Visualization, SAM, BAM, Oneliner, NGS, metagenomics

    442 days ago