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Hi I'm trying to run import-rna with raw read counts. The results are very different from that by targeted DNA seq. The samples for RNA seq vs. DNA seq are 99% same so they are supposed to generate si…
laopp updated
5 years ago
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I have installed TS on my ubuntu 14.04 successfully, but i am unable to find instructions for starting analysis on this. Can anyone please provide some material , how to use it for analysis of targete…
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Hi, I separately tried running `gencore` on a paired-end sequencing run
```
gencore -i mix_2lines_PE.bam -o gencore_out.bam -r $fasta -s 1
```
The input `.bam` file is `738MB`. The output bam …
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Hello,
In order to generate CNA file it was suggested to use the ASCAT tool, unfortunately, we have targeted sequencing data that is not supported by the ASCAT tool yet . What alternative choices…
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Sometimes I just want to trim "from xx bases onward" or "take just the first xx bases". In trimmomatic (considerably slower than atropos) this is obtained with the `HEADCROP` and `CROP` commands, resp…
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Dear,
We succesfully implemented CTAT-splicing in our STAR-fusion pipeline.
**1) we pick up all our relevant fusion genes using STARfusion**
**2) we correctly picked up METx14del,** without fal…
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**LAST EDITED: Aug, 29, 2024**
See parent Epic for further information.
https://github.com/chanzuckerberg/single-cell/issues/644
See current draft for spatial support in SOMA https://docs.goog…
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It would be very useful to report the total number of reads alinged to viral genomes and the fraction of reads aligned to each viral genome with respect to the total number of reads in a sample.
The…
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Hi, I'm new to pyclone and I would like to use it to inferring AML clonal architecture from tumor-only targeted DNA sequencing samples.
I'm not sure how to get information about major and minor c…
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I need help!!
I am using pepper_margin_deepvariant variant calling for my target gene but PEPPER is not recognizing my region of interest where I did targeted sequencing using Nanopore. I think this…