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Incidentally, you will still need to sort the BAM file before indexing it, as GenoMax pointed out.
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Right, you should also get the latest version of TopHat that comes bundled with the appropriate version of samtools required by TopHat.
You'll then have the best of best worlds, the latest version of TopHat running with a tried and tested version of samtools, and the latest version of samtools with all the new bells and whistles.
I'm basing all these assumptions on Devon Ryan's post, but his explanations are quite convincing and his description of the bug corresponds to yours.
My advice:
1- Install the very latest version of samtools with all the new bells and whistles, and without the bug.
2- Install the latest version of TopHat2 which comes bundled with a tried and tested version of samtools, that has been tested for compatibility with TopHat2. (This version will be used internally by TopHat.)
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No harm in trying the latest samtools but TopHat page has this to say
Removed SAMtools as an external dependency in order to avoid incompatibility issues with recent and future changes of SAMtools and its code library (an older, stable SAMtools version is now packaged with TopHat)
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Devon Ryan seems to describe the bug here.
I would just install samtools 1.1 which has many interesting new features anyway.
It should fix the issue.
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Is this the version bundled with TopHat code (which is the one tested to work)?
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Originally posted by GenoMax View PostWhich version of samtools are you using?
Originally posted by GenoMax View PostIs sorting process making temporary files (with names containing 0001.bam etc) before you get that error?
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Can you sort using this command
Code:$ samtools sort ./accepted_hits.bam accepted_hits_sorted
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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!
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