Roger Mulet

Hi, I have noticed that whenever I use `seqDist` with non-default options, `seqCluster` returns the following warning message. ``` In seqCluster(MixcrTest2, distMixcrTest2, .perc_similarity = 0.9) : Number of sequence provided...

Hi, I encountered this error when running CATT for the first time:  However, a quick Google search revealed an easy solution. I only had to change line 587 of...

Add motif_db argument to gimme motifs

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Hi, So far I have been using the default database that comes bundled with Gimmemotifs, which is quite alright for most purposes. However, Jaspar 2018 has just been released and...

FASTA file not found when specifying outputName (JAFFA direct)

1

Hi, I encountered a minor issue when I ran JAFFA direct with the following parameters: `JAFFA/tools/bin/bpipe run -n 15 -p outputName=5360r_jaffa_results -p jaffa_output=jaffa/` The pipeline was interrupted because the "jaffa_results.fasta"...

Trim_galore: number of pairs filtered by length cutoff

9

### Description of feature Hi, The `cutadapt` module works fine for most of the output from Trim Galore!, but apparently it does not capture the number of paired-end reads that...

Long lists of candidate fusions when read length exceeds 100 bp

1

Hi, First of all, thanks a lot for creating this awesome tool. It has proven to be extremely valuable to detect some hard fusions, like IGH::CRLF2 and others involving the...

Hi, I am using Mutect2 (GATK-4.6.2) to call variants in RNA-seq data that have been processed with SplitNCigar. As a result, when a variant is at the beginning or end...