Quote:
Originally Posted by billstevens
You didn't actually convert it to .sam. You should have wrote
samtools view accepted_hits.bam accepted_hits.sam
And then sort the acccepted_hits.sam file
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Thank you, but I have used the same command, I mean like this :
samtools view accepted_hits.bam | htseq-count - /hg19/Annotation/Genes/genes.gtf > count.txt
for the single end dataset which did not ask for sorting and it worked.
Althigh I tried your advice and again there were more errors like :
[bam_index_load] fail to load BAM index.
[main_samview] random alignment retrieval only works for indexed BAM files.
And then I indexed the file : samtools index accepted_hits.bam
And then :
$ samtools view accepted_hits.bam.bai accepted_hits.sam
[bam_header_read] EOF marker is absent.
[bam_header_read] invalid BAM binary header (this is not a BAM file).
[main_samview] fail to read the header from "accepted_hits.bam.bai".
The bam file I am using is the tophat output and I did not approach this problem of indexing and so on with this kind of result
