-
Notifications
You must be signed in to change notification settings - Fork 145
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
chromap chipseq default mode remove duplicates making preseq fail #288
Comments
We are already removing duplicates with Picard MarkDuplicates right? If so, I would be tempted to use that to remove duplicates before running any downstream peak callers for consistency. This would mean switching off any automatic duplicate removal in tools like MAC2 and Chromap. |
Yes, the only thing is that chromap is not a peak caller but an aligner specially meant for aligning ChIP-seq, ATAC-seq and similar (https://github.com/haowenz/chromap). That is why I was wondering whether to switch the removal of duplicates since in fact the chromap step is placed upstream of the Picard MarkDuplicates. Anyway, I think I will switch off the removal of duplicates for this release and keep this issue open so that we can take this point into consideration in following releases. |
Sounds sensible 👍🏽 If we use a single tool like Picard Markduplicates to remove the duplicates then it will be easier to benchmark and compare results downstream. |
Closed by #290 |
As mentioned above, the
--preset chip
argument ofchromap
includes the removal of duplicates (--remove-pcr-duplicates
set by the preset) and thus, the downstreamPRESEQ_LCEXTRAP
process fails with the following error:ERROR: max count before zero is less than min required count (4) duplicates removed
To fix this issue we could use chromap with the arguments included by the
--preset chip
without including the--remove-pcr-duplicates
argument and keep all the rest of the code as it is now for consistency or otherwise, we could keep the removal of duplicates and just skip the affected downstream steps (which seems more optimal). What do you think @drpatelh ?The text was updated successfully, but these errors were encountered: