Comments (4)
alauring
commented on August 15, 2024
Thanks for the comment. We had some issues with this ourselves and were able to get a workaround with the folks who manage our cluster. Feel free to fork our repository and use BiocManager. Please let us know if that provides a more robust solution and perhaps send a pull request?
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grendon
commented on August 15, 2024
I am trying my luck with modules and nextflow instead of using your approach with conda and packrat. If I get anywhere I will be happy to post my version as a branch (perhaps?)
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grendon
commented on August 15, 2024
Would it be possible for you to post results files within the tutorial
so that we can compare our results to your, please?
This is what deepsnv is generating for us in the output.csv file:
| chr | pos | ref | var | p.val | freq.var | sigma2.freq.var | n.tst.fw | cov.tst.fw | n.tst.bw | cov.tst.bw | n.ctrl.fw | cov.ctrl.fw | n.ctrl.bw | cov.ctrl.bw | raw.p.val | Id | mutation |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| HA | 784 | A | G | 0 | 1 | 0.000697 | 1018 | 1018 | 416 | 416 | 0 | 1146 | 0 | 215 | 0 | HA-22_S7_L001 | HA_A784G |
| M | 4 | G | A | 0.008994 | 0.147545 | 0.000885 | 421 | 883 | 1 | 3 | 309 | 937 | 2 | 9 | 1.66E-07 | HA-22_S7_L001 | M_G4A |
| NP | 4 | G | A | 0.000134 | 0.192342 | 0.001148 | 334 | 725 | 1 | 3 | 138 | 518 | 1 | 1 | 2.47E-09 | HA-22_S7_L001 | NP_G4A |
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alauring
commented on August 15, 2024
That looks like a typical output file for DeepSNV. I do not know if the data are exactly like what we get in our tutorial, but suspect that everything is working properly here!
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Related Issues (8)
- Can't reproduce results of tutorial, too many variants with p.val=NA HOT 4
- deepSNV.r generates output.csv files with different column order - why? HOT 3
- control.bam HOT 6
- adding results files to the tutorial for comparison HOT 1
- reciprocal_variants.py throws error HOT 6
- File headings in sum.csv is wrong
- update tutorial HOT 1
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