Dereje Jima
Dereje Jima
Attached [test_files.zip](https://github.com/bedops/bedops/files/2634566/test_files.zip)
Hi Shane, Thanks you very much!! This is exactly what I was looking for. Appreciate it!!!! Dereje On Fri, Nov 30, 2018 at 3:54 PM Shane Neph wrote: > There...
For the current work, showing pileup and splicing junction is necessary. I can convert the bam file to any format such as wig, bigwig or bedGraph. I installed as an...
changed under preference to use binary but now I got "unknown workaround: 'nonodelay' with sshfs
Looks like -o workround: 'nonodelay' not an option in sshfs
> java --version openjdk 11.0.1 2018-10-16 LTS OpenJDK Runtime Environment Zulu11.2+3 (build 11.0.1+13-LTS) OpenJDK 64-Bit Server VM Zulu11.2+3 (build 11.0.1+13-LTS, mixed mode)
This fixed the error: `--snap-map --snap-pre` Add to the doc
@ArtRand I am confused by this `--segment `. What passes as `segments_fp.` That had to be dynamically handled based on sliding windows. @demis001
@ArtRand Sorry, I have an additional question: ``` modkit dmr pair -a ${BASECALL_DIR}/wild_final_merged_sorted.bed.gz \ -b ${BASECALL_DIR}/captive_final_merged_sorted.bed.gz \ -o ${BASECALL_DIR}/DMR_wild_captive.bed --ref ${REF} --base C \ --threads 16 --log-filepath ${BASECALL_DIR}/dmr_call.log ``` ###...
I passed ` --segment my_segment.bed` to the above command. If I am not mistaken, this file documented the DMR, and the `-o out.bed` is the DMC. Please confirm.