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Old 12-05-2014, 11:40 AM   #1
stormin
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Location: US

Join Date: Aug 2014
Posts: 23
Default indexing tophat bam files

Hi,

I am having trouble using samtools to index my tophat output for IGV viewing. The tophat output bam should be sorted (although I am having trouble too using samtools to sort the tophat output bam file).

This is how I call the tophat:
tophat2 -M --b2-very-sensitive --GTF ~/Documents/transcriptome_gtf/genes.gtf -p 7 --read-realign-edit-dist 0 --output-dir ./example ~/Documents/genome_UCSC/genome ~/Documents/Data/example.fastq

I then call samtools indexing using:
samtools index accepted_hits.bam

But I would get this error:
[bam_index_build2] fail to create the index file.

Doing samtools sorting with below command give me this error:
samtools sort ./accepted_hits.bam sort.prefix

[bam_sort_core] merging from 12 files...
open: No such file or directory
[bam_merge_core] fail to open file sort.prefix.0000.bam

At this point, I'm not sure what is going on. Please help!

Zach
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