Closed DarioS closed 7 years ago
Hi,
When you specify the --forward-prob option to RSEM are you also using the --strand-specific option? If so, try omitting the --strand-specific option, which I believe forces --forward-prob 1.
In summary, try just --forward-prob 0 without the --strand-specific option.
Colin
On Sep 23, 2016, at 2:00 AM, DarioS notifications@github.com<mailto:notifications@github.com> wrote:
I use the --paired-end and --strand-specific options to map to the GENCODE Genes 25 transcriptome with Bowtie.
For --forward-prob 0 I get 2.79 % of reads mapped, for --forward-prob 1 I again get 2.79 % and when all of the strand specific options are left out of the command, I get 79.99 % mapped reads.
I have also mapped with STAR to the genome, and the mapping percentage is high and the reads are clearly strand-specific when viewed in IGV and coloured by strand of the first read in the pair. Why is the mapping percentage so low with the stand-specific approach to RSEM and Bowtie ? Also, using --forward-prob 0 and --forward-prob 1 should not produce identical mapping percentages. Are they being ignored in the code ?
I am using version 1.2.31.
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Thanks; the workaround is sufficient. But, it's a bit unexpected from an end user's perspective that --strand-specific
dominates the setting of --forward-prob
. Perhaps this could be changed, or at least explicitly documented. If --forward-prob
was deprecated and --strand-specific
was replaced by --strandedness
and had none
, forward
, and reverse
as the three acceptable values, it would be unambiguous and concise. It's also currently unlcear what happens if the user provide a value like 0.30
for --forward-prob
, which is meaningless.
Hi @DarioS, thanks for your suggestions! I have added --strandedness 'none/forward/reverse' option and deprecated --strand-specific and --forward-prob options. This will be reflected in the next release of RSEM.
Thanks, Bo
I use the
--paired-end
and--strand-specific
options to map to the GENCODE Genes 25 transcriptome with Bowtie.For
--forward-prob 0
I get 2.79 % of reads mapped, for--forward-prob 1
I again get 2.79 % and when all of the strand specific options are left out of the command, I get 79.99 % mapped reads.I have also mapped with STAR to the genome, and the mapping percentage is high and the reads are clearly strand-specific when viewed in IGV and coloured by strand of the first read in the pair. Why is the mapping percentage so low with the stand-specific approach to RSEM and Bowtie ? Also, using
--forward-prob 0
and--forward-prob 1
should not produce identical mapping percentages. Are they being ignored in the code ?I am using version 1.2.31.