Convert sra to bam file error handling

Question

[c12i34]

Hi Guys,I am trying to convert some sra files into bam format. At the moment, I am using this command from sratoolkit

sam-dump SRR390728 | samtools view -bS - > SRR390728.bam

but unfortunately I got an error message like this:

sam-dump.2.4.2 err: param invalid while validating file within file system module - content-size read from local file is invalid.

Having said that, I still get a bam file as output at the end. Can I ignore that error msg and continue with peak calling? Also how I can convert multiple sra files to bam in one go? Many thanks!

[Ram]

I do hope you took a look at this post: Sra Format Questions: How To Get A Sam File That Can Be Converted To Bam?

Answer 1

[gauravsingh.singh86]

sam-dump SRR390728.sra  > SRR390728.sam

Once you have your SAM file:

module load SAMTools
samtools view -b -S SRR390728.sam > SRR390728.bam

[Devon Ryan]

Note that loading samtools as a module will be completely system dependent and often not required.

[Ram]

What Devon said. module load samtools is only valid in shared environments. Also, OP is using the latest version of samtools so a direct conversion to BAM should not be the cause of the problem.