Issues with output from quantification step
jpgvtech opened this issue · 5 comments
Hi we build the graph using the gtf and the genome fasta for GRCh38. However when we run the quantification the count matrix looks like we are only getting results to the odd chromosomes at the end of the reference:
Transcript Count
KI270412 1
KI270382 1
KI270539 1
KI270311 4
KI270334 1
KI270522 10
KI270381 32
KI270580 2
KI270340 1
KI270429 4
KI270418 1
KI270389 3
KI270364 25
KI270515 2
KI270375 1
KI270420 3
The documentation is slightly confusing. For graph building we want genome fasta (1 sequence per chromosome) and gtf. Then for quantification in the config file its the transcripts fasta the same genome fasta file or do you need to give the transcripts as separate fasta sequences?
Hello,
I think I understand your confusion. In the Readme where the necessary input files for the quantification step were described, we accidentally used the word reference sequence, when we were talking about the transcripts.fa file (parameter called transcripts mentioned in the parameter table).
Please run the the quantification step with supplying the transcripts.fa file in the config.yaml file. Then it should work.
I have fixed that in the Readme and hope that this confusion can now be avoided.
Hope that helps,
Marcel
Dear Jane,
how many threads are you using? Try to use fewer threads for the fusion step, that should reduce the memory consumption.
Hope that helps,
Marcel
Dear Jane,
we have fixed the problem with the PickAdjacentAlnPairs binary, which was indeed using more memory than it should have. Please update your local version and try again.
Hope it solves the problem,
Marcel