XenoCP

[adamdingliang]

Documentation for XenoCP pipeline.

[mtreadwa]

Ling in the inputs table did you mean "buckets"?

[claymcleod]

Also, Adam, we need to ensure that the .idea files aren’t added to the repo. Please remove them before merging.

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On Apr 29, 2019, at 5:06 PM, mtreadwa ***@***.***> wrote: @mtreadwa requested changes on this pull request. Ling in the inputs table did you mean "buckets"? — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or mute the thread.

[adamdingliang]

Fixed the typos and removed .idea files.

[agout]

In addition to my edits, I've made a few comments below....

1. In the input table: when you refer to Mates in the input....do you mean read-pairs? or mate read pairs?
2. In the input table: what is "Mate suffix length" this isn't clear to me...
3. In the input table: what are buckets? this isn't clear to me from this explanation - need to provide further description in the input table.
4. In the process diagram you say "Original Human Bam" but I think you mean Xenograft BAM? Need to be consistent with the description at the start.
5. In the process diagram, I don't think you've represented clearly what happens....it seems like once you align a read to the mouse genome, you make a determination whether it maps best to the human or mouse genomes....and then act accordingly...however this isn't represented in the flow diagram succinctly (step 3 of process explanation)
6. In the process diagram - CLR is an abbreviation for List of Contaminated Reads? if so this acronym doesn't quote make sense.

[adamdingliang]

@agout thanks for the comments. Responses to the questions:

1. yes, paired-reads.
2. "Mate suffix length" is read name suffix length. The split step of the workflow also trims the unnecessary read name suffixes such as /1 and /2. It allows users to choose the suffix length to trim. I have modified the description to "Length of read name suffixes to be trimmed. [default: 3]". Hope it is clear.
3. Updated the description to "Number of buckets to split original bam to for parallelism [default: 31]"
4. Updated the workflow image.
5. There are rules to determine it aligns better to human or mouse. I don't think we can put rules in the diagram. So no good idea of how to make it better. Any further suggestion?
6. Yes. Change to LCRs to be clear.

[agout]

thanks Adam and Madison

[adamdingliang]

Thanks very much, Alex and Madison.