skip adapter-trimming

[ginolhac]

If I want to map the reads as they are in the raw FASTQ. How should I do? In the makefile I think I can use the syntax (for single-end reads)

Single: path/raw.fastq.gz

so paleomix should consider them as already trimmed. But, could trimming be an additional feature?

[MikkelSchubert]

I'm afraid that I do not understand exactly what you are asking. You can skip the trimming step, mapping the reads as-is, if you specify them as you've shown. This works for all read types:

LaneName: Single: path/raw.fastq.gz Paired: path/raw.{Pair}.fastq.gz Collapsed: path/raw.collapsed.fastq.gz

However, I am not sure what you mean by "could trimming be an additional feature". If you want the reads to be trimmed, then you'd just write them normally:

LaneName: path/raw.fastq.gz

Cheers

On Wed, Feb 17, 2016 at 9:36 AM Aurélien Ginolhac notifications@github.com wrote:

If I want to map the reads as they are in the raw FASTQ. How should I do? In the makefile I think I can use the syntax (for single-end reads)

Single: path/raw.fastq.gz

so paleomix should consider them as already trimmed. But, could trimming be an additional feature?

— Reply to this email directly or view it on GitHub https://github.com/MikkelSchubert/paleomix/issues/7.

[ginolhac]

I was thinking having a Feature just like

  # To disable all features, replace with line "Features: []"
  Features:
    - Trim reads
    - Raw BAM        # Generate BAM from the raw libraries (no indel realignment)
                     #   Location: {Destination}/{Target}.{Genome}.bam
#    - Realigned BAM 

but forget about it. I used the old fashion way that worked out nicely.