Amina Echchiki comments

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                                            Amina Echchiki

graphmap spliced alpha: no spliced alignments reported

Hi Ivan, I ran the following command: `/home/aechchik/graphmap/bin/graphmap-not_release align -x rnaseq -t 16 -r reference-genome.fa -d reference-transcripts.fasta -o graphmap_ref.sam` where: - `reference-genome.fa` is a concatenation of chromosomal genome files at:...

Cufflinks is frozen at 14%

Hi @RxLoutre . I am doing basically the same thing as you, but with data from D. melanogaster, and I experienced the same issue as you: check [here](https://groups.google.com/forum/#!topic/tuxedo-tools-users/eU-sAUWOHEQ). I got...

marginPhase error: Assertion `seqLen >= rProbs->length + rProbs->refStart' failed.

FYI, just discovered that another program that I run in parallel failed because I was running out of disk space. Maybe that can be the cause. Will keep you updated...

marginPhase error: Assertion `seqLen >= rProbs->length + rProbs->refStart' failed.

Hi @benedictpaten, thanks for the reply. well, for my original run, I really believe that the reference fed as assembly (input fasta) and as mapping reference for the reads (input...