Paleomix output reads folder no fastq reads

[xuefenfei712]

Hi

Thanks for your useful tool. It is much more convenience for mapping. In my side, I use AdapterRemoval2 to trim the ancient PE reads, and have truncated reads. Then I use paleomix 1.12.3 for Adapterremoval and mapping, while I found in my output folder of reads, I donot have the truncated reads, but reads stastics instead. If I understand correct, it's because I truncated my reads already and paleomix output only have the stastics report, which indicates the path to it.

Thanks for your time.

best

Xue

[xuefenfei712]

Also I want to know the bam file from paleomix 1.3.8 is sorted or not, if I want to realignment, is it possible to use paleomix, thankyou!

[MikkelSchubert]

Hi Xue,

Sorry for the late reply. If you are specifying that you have already trimmed reads in the YAML file, then adapter removal will not attempt to (trim and) merge them. Instead all it does is validate that the files are good and collect a few statistics. If you want to merge the reads, then I'd recommend starting the with original, untrimmed reads. The program used by paleomix for trimming/merging does not currently support only merging reads, so results would be worse than if you started from the original, untrimmed reads.

The final BAM files produced by paleomix are sorted by position, so you should be able to perform realignment on them.

Best, Mikkel