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Dear,
I want to run the PASA alignment assembly pipeline using a very genome which has very long trons such as longer than 20kb. I run the pipeline, some errors occur, I want to know whether this err…
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ABRA version - 0.96
Platform - CentOS
command used to run ABRA
`java -Xmx4G -jar abra-0.96-SNAPSHOT-jar-with-dependencies.jar --in C26.bam --out C26.ABRA.bam --ref hs37d5.fa --targets Agilent_Nimblege…
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Working through a dataset, I found that most of the resulting alignments only included 100K-200K sequence identifiers from the input dataset even though most of my samples have >1M sequences. Unsure o…
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Hello!
When it comes to structural variant calling, one characteristic of the presence thereof is a noisier sequence than usual. With these noisy sequences, the secondary alignment can then provide…
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- [ ] Try running with different levels of search depth (-k 32, 64, etc.) in bowtie2
- [ ] Compare to smith-waterman
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Hello,
I am mapping some paired-end strand-specific RNA-seq. This data maps logically with STAR, with the majority of reads in sense with their transcript. However, this is not the case in Magic-B…
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Which language we can add already?:
- Ukrainian
- Russian
- Polish
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```
...BOWTIE PE is still running ..from one week! No errors, seems that there are
no progress in the output stream. I attach it. The input reads are the same I
used for the other modules: did you h…
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At present, featureCounts, when passed a collection, outputs a collection of vectors. E.g. it does
```
featureCounts 1.bam
featureCounts 2.bam
...
featureCounts n.bam
```
However, the featureCo…
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This is not really a bug as the documentation clearly states how deduplicate_bismark expects UMIs to be handled, but it is an easy mistake to make.
As documented in deduplicate_bismark, Bismark expe…