To View A Srr038263.Sra Bam File In Samtools

Question

[Rocky]

I would like to view a SRR038263.sra BAM file in samtools and do alignment to reference genome. How could I view the SRR038263.sra in samtools? I have already install and make samtools at same directory where I have SRR038263.sra BAM file. I would be glad for your kindness and support.

Regards, Rocky

Answer 1

[Fabian Bull]

The Sequence Read Archive (SRA) stores raw next-gen sequencing data.

BAM is the compressed binary version of the Sequence Alignment/Map (SAM) format, a compact and index-able representation of nucleotide sequence alignments.

I would be supprised if an alignment could be stored in a SRA file. What you probably want is extact the sequence data. For a guide see: http://www.ncbi.nlm.nih.gov/books/NBK47540/

Afterwards you can map the reads against a reference and gain a BAM file.

[Casey Bergman]

The link to link to the NCBI book referenced above it out of date. To extract data from an SRA submission, I recommend following advice in this biostar thread.