Option confusion for region_p

[tomh1lll]

When running comb-p pipeline, the command generates an empty regions-p.bed.gz file. I have attempted to run comb-p region_p by itself but it keeps crashing, likely because I'm not sure what should be the input for -p or -r for this program. Would you be able to provide an example for these files to use as test data? Or at least provide examples of the first few lines of each file in the reply, so I can generate my own test data.

Additionally, the test fastqs you provide links to is no longer available, would you be able to provide examples of the bed files generated by this pipeline?

Thanks

[brentp]

Hi, there are examples here with a readme in each of those directories. If you have any questions about those examples let me know.

If you show the command that you ran along with the messages that were shown, that would give more information in order to help you.

[tomh1lll]

Thanks for the quick reply.

I get the following (and similar) responses when trying to download your data.

--2022-02-08 11:02:43--  http://dzlab.pmb.berkeley.edu:8080/work/GEO_submission/raw/WT_endosperm_BS_seq_raw_batch-1.2.fastq
--2022-02-08 11:02:43--  http://dzlab.pmb.berkeley.edu:8080/work/GEO_submission/raw/WT_endosperm_BS_seq_raw_batch-1.1.fastq
Resolving dtn01-e0 (dtn01-e0)... Resolving dtn01-e0 (dtn01-e0)... 10.1.200.237
Connecting to dtn01-e0 (dtn01-e0)|10.1.200.237|:3128... 10.1.200.237
Connecting to dtn01-e0 (dtn01-e0)|10.1.200.237|:3128... connected.
Proxy request sent, awaiting response... connected.
Proxy request sent, awaiting response... 503 Service Unavailable
503 Service Unavailable
2022-02-08 11:02:43 ERROR 503: Service Unavailable.

2022-02-08 11:02:43 ERROR 503: Service Unavailable.

[1]+  Exit 8                  wget -O - http://dzlab.pmb.berkeley.edu:8080/work/GEO_submission/raw/WT_endosperm_BS_seq_raw_batch-${i}.1.fastq >> ${READSA}_1.fastq
[1] 33449
--2022-02-08 11:02:43--  http://dzlab.pmb.berkeley.edu:8080/work/GEO_submission/raw/Embryo_BS_seq_raw_batch-1.1.fastq
Resolving dtn01-e0 (dtn01-e0)... 10.1.200.237
Connecting to dtn01-e0 (dtn01-e0)|10.1.200.237|:3128... connected.
Proxy request sent, awaiting response... --2022-02-08 11:02:43--  http://dzlab.pmb.berkeley.edu:8080/work/GEO_submission/raw/Embryo_BS_seq_raw_batch-1.2.fastq
Resolving dtn01-e0 (dtn01-e0)... 10.1.200.237
Connecting to dtn01-e0 (dtn01-e0)|10.1.200.237|:3128... connected.
Proxy request sent, awaiting response... 503 Service Unavailable
2022-02-08 11:02:43 ERROR 503: Service Unavailable.

I was just wondering if you could provide the comb-P input file directly to speed things up for users (the embryo-endo.fisher.bed file), as the file is likely small & easily available to you, instead of the hassle of trying to generate the file myself. This file isn't in the examples/bsseq/data folder in this github, but I would expect it to be.

[brentp]

here are other files: https://github.com/brentp/combined-pvalues/tree/master/examples/fake/