On 07/10/15 12:29, Sandeep Marla wrote:
I am using GSNAP and samtools for my RNA_Seq analysis. I got the error
*"[E::hts_idx_push] NO_COOR reads not in a single block at the end 2
-1”. * Below are the commands that I have used and the error message.
Your help will be really appreciated in resolving this problem.
*Command line*:
....
${HOME}/software/samtools view -bS $out.sam -o $out.tmp
${HOME}/software/samtools *sort -n *$out.tmp $out
${HOME}/software/samtools index $out.bam
I don't think you should have used the name "-n" option to sort - the
file should be coordinate sorted for index to work.
--
The Wellcome Trust Sanger Institute is operated by Genome Research
Limited, a charity registered in England with number 1021457 and a
company registered in England with number 2742969, whose registered
office is 215 Euston Road, London, NW1 2BE. ------------------------------------------------------------------------------
_______________________________________________
Samtools-help mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/samtools-help
