Patrick Roelli

Great. This shows that you need to use the `--sliding-window` option and I'd recommend adding `--start-trim`. The value of the start trim should be around the mean number of bases...

Hello @ZeyanZhang, sorry I kind of forgot to come back to you. The logs you're showing me should provide some mapped content. Have you tried the dev branch?

@YunZheHuang Would you mind sending me a sample of the data so that I can look at it?

@GrigoriiNos in the documentation there is a section about [special cases](https://hoohm.github.io/CITE-seq-Count/Running-the-script/#filtering) You need to use the `--start-trim` with 10

Hey @vlink I think there is in issue with indexes. It seems like your sequences start at base 2 on R2. Can you try this command: `zcat short_HTO_index_S6_combined_R2.fastq.gz | head...

There is still something strange here: ``` TACCCACAGGGAGGGT TGTGATCAAGTAACCCACCAGTAAGAC TACCCACAGGGAGGGT TGTGATCAAG ACCCACCAGTAAGAC ``` Where is this TA coming from?

I think you might need to change your `-umil` to 12

The warning is only a warning. It mostly comes from the fact that people sequence a bit deeper than what they need to, in your case, it's probably a wrong...

Hello, what happens if you run fewer reads? Do you still get the same error? On Wed, 27 Oct 2021 at 02:28, fjrossello ***@***.***> wrote: > Hi, > > I...

I'm assuming it might be related to the way your paths are called. Have you tried giving them directly as a harcoded path?