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Hi Yuanhua,
I am using v2.2 to count other types of AS, A3SS for example:
brie-count -a ~/genome/mm10/mouseAS/A3SS.gff3 -o . -S bamfile.list -p 8 -t Any
Even with -t Any option, this comma…
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Hi
I am trying to run lumpy of ~150 yeast genomes. For some of the samples I get the following error:
[danaba@molgen all_P]$ lumpyexpress -B remove/evoP1_P20.all.mdup.sort.bam -S remove/evoP1_P20.spli…
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Bismark_mapping Failed, Run time 08:18:26, OUT_OF_MEMORY.
Please see code
bismark --genome_folder genomes/bismark -o bam/ --non_directional --parallel 8 --score_min L,-0.6,-0.6 -1 trimmed/${base1}…
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Hello,
I wanted to look at protein presence-absence of a broader group of genomes (several different orders from alpha-proteobacteria). Would you say it's possible with panX, or should I just run …
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The Ginkgo genome is about 9.8GB, and I tried to build index in hisat2-build with the parameters **--ss** and **--exon**
however, two times when I run this task， it was killed without any alert， th…
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Vulnerable Library - log4j-core-2.14.0.jar
The Apache Log4j Implementation
Library home page: https://logging.apache.org/log4j/2.x/
Path to dependency file: /biojava-genome/pom.xml
Path to vulnerabl…
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### Description of feature
Hello,
Would it be possible not to instruct Bismark methylation extractor to use both the --comprehensive and --merge_non_CpG flags when specifying --comprehensive to t…
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Hi,
I tried to run rascaf using **sorted bam file** (which is generated by mapping trimmed RNA-Seq data to draft genome assembly scaffold) and **draft genome assembly** with cmd:
~/rascaf/rascaf -b…
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Hi,
An error (OSError: [Errno 28] No space left on device) occurred when running exonerate.
I checked my device, it looks like there is plenty of space left.
Filesystem Size Used Avail Use…
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Hello group!
I met a problem when I run
```
rsem-generate-ngvector ${REF} ${ROAD}/genome/wheat_ref
rsem-for-ebseq-calculate-clustering-info 25 /storage/yifang/20190405_RNAseq/data/rsem/genome/w…