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The SRA related code that was recently accepted as part of #323 has caused too many issues, is tarnishing the reputation of HTSJDK and projects which depend upon it and is a big step in the wrong dire…
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Hi,
First of all, thank you for developing this amazing tool!
I have encountered a discrepancy in the `inStrain profile` results regarding gene mapping at the same positions between different sa…
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Hello,
I noticed Freebayes missed a call at position chr9:133738406 and from this point on it skipped also other calls, which are clearly visible from the bam file. Here what I see in the log file an…
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Thanks for this great tool.
When multiple annotations are too close together (like within 10000 bases) in one chromosome as shown in , only one of them could be visible. Is there any way to zoom i…
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Hi,
I met a problem, the BUSCO score decrease after update.
The BUSCO v5 score was 91% after EVM (based peotein model).
Next,I performed PASA pipline to update my annotation with default parameter…
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I tried to simulate 1000 Inverted Duplication (IDUP) events with PacBio reads using hg38 genome, but the reads do not seem to contain any such events. I aligned the reads with pbmm2, and can't see any…
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I am looking for the MACS2 p-value signal for every base-pair, similar to the bigwigs available from [ROADMAP](https://egg2.wustl.edu/roadmap/data/byFileType/signal/consolidated/macs2signal/pval/) or …
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Version 4.1.0 output file known_miRNAs.gff3 not displaying correctly on IGV. Possibly caused when the same ID is present more than once on the same chromosome.
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**Use case**
I run macs2 with below command per q-value cut-off 0.05, 0.1 and 0.5
`macs2 callpeak -f BAMPE -g hs -n sample_ID -t sample_remove_duplicate_mito.bam --outdir ./peak --min-length 100 --q…
khsjh updated
9 months ago
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