Tobias Neumann

Sorry lost track of this: Can you let me know if there is anything written in the log files in the map folder?

Ok I suppose the 5 samples worked also because I dont see an error in the log files. Can you try to only run it on the failed samples and...

Did you get any error messages for those files? How do the input fastq files look like?

Ok how does your bed file look? Look like there's the strand information missing.

Yes you miss the score column after the gene id - check out the official bed format. you can put the score to 1000, slamdunk doesnt really look at it.

Can you send the qc files for this observation? This sounds not right.

Like where to you see that you have more T>C conversions in your untreated sample compare to the labelled ones.

Yes that indeed looks like you have way more conversions in your untreated sample. U sure there was no sample swap or anything?

Do you get any errors on the console or log files?

Can you send the exact commands you run? It is very weird that you would have bamIndex files that are older than the actual bam files.