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
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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