Amina Echchiki

graphmap spliced alpha: no spliced alignments reported

2

Hi Ivan, we tested Graphmap to align RNA-seq reads to the reference genome. For benchmark purposes, we tried to align the [reference transcripts](ftp://ftp.ensembl.org/pub/release-89/gtf/drosophila_melanogaster/Drosophila_melanogaster.BDGP6.89.gtf.gz) in fasta format on the [reference genome](ftp://ftp.ensembl.org/pub/release-89/fasta/drosophila_melanogaster/dna/),...

Test data not available

2

Hi. I was trying to test a Cufflinks server installation, but the link you provide in the readme for downloading testing data is broken: ``` $ wget http://cufflinks.cbcb.umd.edu/downloads/test_data.sam --2016-08-03 14:29:03--...

Hi, I'd like to report a probable consideration for an update in Cufflinks manual (http://cole-trapnell-lab.github.io/cufflinks/cufflinks/index.html). I hope this is the correct place to do this. As I am using a...

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

10

Hi @benedictpaten do you know what would cause error `Assertion seqLen >= rProbs->length + rProbs->refStart' failed.` ? here is the execution log: ``` aechchik@dee-serv07:/scratch/beegfs/monthly/aechchik/amphioxus/mp$ ../../build/marginPhase /scratch/beegfs/monthly/aechchik/amphioxus/mp/reads_to_haploADref.bam /scratch/beegfs/monthly/aechchik/amphioxus/hm2/amphio_A_ref_D.fa marginPhase/params/params.pacbio.json Set log...

Not really an issue, but a documentation possible enhancement, whenever you have time :) 1) maybe mention that the `params` file can be found in the [params folder](https://github.com/benedictpaten/marginPhase/tree/master/params). Also, probably...