ATAC-seq Primers & Adapters

[williamssanders]

Line 46 of ATAC-seq/auyar_scripts.sh:

echo python $scriptDIR/auyar/pyadapter_trim.py -a $outputDIR/trimmomatic/\$FILE1paired -b $outputDIR/trimmomatic/\$FILE2paired >> $outputDIR/trimmomatic.qsub

1. Where did Asli get pyadapter_trim.py from?
2. Does it have a reference/citation?
3. Why are we using this instead of the built in adapter trimming features of Trimmomatic?

If we could get a list of ATAC-seq specific primers and adapters used during the library creation and sequencing process, we could consider using Trimmomatic for adapter trimming and removing this step.

This needs testing and evaluation.

[ucarduygu]

We got this script from the greenleaf lab through personal contact, dont think it is published yet. The main idea behind this script is to shift the atac reads 4 or 5bp from cut ends to account for the 9bp space Tn5 molecule is holding. We noticed that this script is buggy while shifting some reads. However, didnot have the time to fix this. Hopefully we can cut this script from the pipeline in the future and do the shifting using another tool. We can chat more about this in person.