Bismark: -score_min testing

[yaaminiv]

I tested different -score_min options on a subset of the C. virginica data in this Jupyter notebook.

@sr320 Should I produce the summary report now, or should I dedpulicate/sort/index/extract methylation calls before producing the summary? I'm not sure which option would be better for understanding how well the alignment went.

[sr320]

can you provide a simple table showing mapping efficiency with different -score_min s ?

[yaaminiv]

The table can also be found in this lab notebook post.

Sample	L,0,-0.6	L,0,-0.9	L,0,-1.2
1	15.5	20.2	28.8
2	32.4	40.2	49.8
3	37.2	45.3	53.6
4	36.0	44.7	52.9
5	34.6	42.9	51.7
6	36.7	45.0	53.8
7	34.6	42.9	51.4
8	31.7	39.0	47.6
9	33.0	41.2	49.9
10	36.6	44.9	53.0

[sr320]

Were files satisfactorily quality trimmed prior to aligning?

[yaaminiv]

Yes, I used files that @kubu4 quality trimmed.

[sr320]

url for QC pre and post trim?

[yaaminiv]

From Sam's notebook

[sr320]

we need to keep an eye on sample 1..
but go ahead and run full Bismark align w L,0,-1.2 into (and out of) methylkit for DML and DMR