EOF marker is absent in samtools

[dena.dinesh]

HI,

In my RNAseq raw data, I filtered out adapter sequence using fastx and later removed rRNA reads by mapping to rRNA reference file. When I tried to convert unaligned reads from rRNA mapping to bam format, It throws me an error that
[bam_header_read] EOF marker is absent. The input is probably truncated.
[bam_header_read] invalid BAM binary header (this is not a BAM file).
[main_samview] fail to read the header from xxx.sam

I don’t what is the problem and how to tackle it.

Any Ideas or suggestions?

[dpryan]

What's the exact command you used?

[dena.dinesh]

Hi Ryan,

I initially used
samtools view -b control_1.sam > control_1.bam and got the error

then later when I used -T option and providing the path of fasta file

samtools view -b -T /path/to/reference/fasta_file control_1.sam > control_1.bam

it worked but I am not sure whether this approach is right or wrong?

[dpryan]

The input is SAM formatted, so you need the -S switch:

samtools view -Sb control_1.sam > control_1.bam

[dena.dinesh]

Thank you Ryan. I tried -Sb option and it worked

Is using -T option and providing reference Transcriptome file is correct?

[dpryan]

No, that'll produce a non-functional file (it's surprising that it didn't produce an error). The purpose of the -T option is if you have a BAM file that doesn't have a header for some reason. Then you can replace it with the information from an indexed fasta file (hopefully the reads were aligned to that fasta file...otherwise the alignments will be to the wrong chromosomes).