SalimMegat

Now it detects 36 fastq but process them as single end....

I directly downloaded the fastq from https://www.ebi.ac.uk/ena/browse/read-download. The files seem to be ok since i have been able to map them with STAR without any problem.. Salim.

Hi, Actually on this run I downloaded the SRA with the script below and converted to fastq [wget_files.txt](https://github.com/LiuzLab/SalmonTE/files/3313252/wget_files.txt) Salim

Hi, I finally decided to run it as single end reads and it worked although I'd really like to understand why this is the only set of fastq where salmonTE...

@hyunhwaj I have downloaded the SRA using the following command: wget ftp://ftp-trace.ncbi.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR692/SRR6924174/SRR6924174.sra -P /b/home/medecine/smegat/ and I converted it to fastq using this command: while read x do fastq-dump -I -v...