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Forum: RNA Sequencing 03-07-2016, 12:16 PM
Replies: 8
Views: 3,589
Posted By moldach
Can anyone help?

Can anyone help?
Forum: RNA Sequencing 03-03-2016, 12:44 PM
Replies: 8
Views: 3,589
Posted By moldach
I had tried mapping at one point some-time-ago to...

I had tried mapping at one point some-time-ago to the closely related un-annotated genome. Unfortunately, I used Bowtie2. I now know better; you need to use a splice-junction aware aligner.



So...
Forum: RNA Sequencing 03-03-2016, 12:06 PM
Replies: 8
Views: 3,589
Posted By moldach
I mapped directly on my transcription assembly. ...

I mapped directly on my transcription assembly.

I couldn't find any reference to getting the number of reads on each transcript (maybe it's just worded differently?) from the documentation of...
Forum: RNA Sequencing 03-02-2016, 10:45 PM
Replies: 8
Views: 3,589
Posted By moldach
Assigning reads to genes in the absence of genomic annotation

I'm looking for a method to calculate read counts from SAM/BAM files that does not require an annotation file (GTF or BED files).

I've done a de novo transcriptome assembly of an organism which...
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