Hi all,
I am trying to run cufflinks on STAR-aligned reads. After converting to BAM and executing "sort" command I do this:...
6 results in 0.0029 seconds.
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Cufflinks: sort order of reads in bams must be the same
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Cufflinks refuses to operate on Tophat2 created bam or sam files due to sorting error
Hi there,
I have really had alot of trouble over the last couple weeks trying to get either Cufflinks 2.0 and 2.1 to accept Tophat 2 (latest... -
A faster read sorter
Hello,
I recently developed a fast stream-based .SAM sorter, streamsorter. It reads .SAM output from a stream (for instance, produced by bwa or...Last edited by brofallon; 04-25-2013, 02:02 PM. -
Why HTseq warning of unfound mate pairs?
Dear all
I am using htseq-count tool to summarize gene counts from bam files generated by tophat (v 2.03) based on bowtie2. I've used this pipeline... -
Problem merging BAM files
Hi everyone. We are having difficulty merging BAM files. Our pipeline so far is this:-
50bp single-end rna-seq reads - map to hg19 with... -
sorting bam files
Hi,
I have run a bowtie followed by a tophat with the unmapped reads.
I than want to merge the two sam files (output)....
