Hi,
I have been sorting tophat generated .bam files with samtools to use them as
input for htseq-count.
$ samtools sort -n file1.bam -o file1.bam_sorted_n.bam
for 36 of 39 files this works fine, while for 3 files i receive the following
error:
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated.
These 3 files happens to be the largest files of ~ 4Gb
any suggestions? Can I check if the files are corrupt or if it is a bug in
samtools?
Thanks
-Jens
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