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Hi,
I am working with WGBS data on a non-model organism. I used Bismark (with Bowtie) to align my reads and would like to use Methylpy to identify DMRs. I installed methylpy in a conda environment…
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In the `.calculateBamCoverageByInterval()` function:
```r
.calculateBamCoverageByInterval
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```diff
$ git checkout develop
$ git --no-pager diff 2020-05-26 -- scripts/Align_mem.sh
diff --git a/scripts/Align_mem.sh b/scripts/Align_mem.sh
index c306a17..7e03c07 100755
--- a/scripts/Align_…
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Hi,
I installed Variant Detective to work on bacterial genomes and found that Claire3 is not working - even with the test dataset.
Any idea what causes this behavior.
I have copied the log below fo…
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I am trying to train ChromBPNet on Arabidopsis ATAC-seq data, but run into the error `"Input file shifts inconsistent"` as in #153, #174 and #176. Having read through these other issues, I was able to…
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Will it be useful to add filter for tags, such as "[NH]>1" to filter reads of multiple hits? Will the same grammar as `--input-fmt-option` of samtools help?
Thank you.
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**Version info**
- bcbio version (`bcbio_nextgen.py --version`): v1.2.9
- OS name and version (`lsb_release -ds`): Red Hat Enterprise Linux release 8.5 (Ootpa)
**To Reproduce**
Exact bcbio comma…
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hi ，I have ran ALLhic with such error, i do not know how to fix it ,my orders and the error.log are as follow:
bwa index draft.asm.fasta
samtools faidx draft.asm.fasta &
bwa aln -t 10 draft.asm.fa…
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In my Amazon EC2 instance I have the following:
ubuntu@ip-333-31-16-230:~$ df -h
Filesystem Size Used Avail Use% Mounted on
udev 79G 0 79G 0% /dev
t…