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For Illumina sequencing, we have R1 and R2 fastq files for one sample? How to deal with these paired-end sequencing file? Should I merge R1 and R2 first, then use SmaltAlign to do align?
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We agreed in our Poseidon meetings that we would soon upgrade our schema to allow for an additional optional file for Poseidon packages, named `sequencingSourceFile`. The file will be a tab-separated …
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Previously we have not included a plot that gives us a histogram of read lengths because most of our reads have been Illumina reads with a fixed cycle length per run. With 3rd generation platforms rea…
mp15 updated
9 months ago
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>Description: The median absolute deviation of sequencing coverage derived from short paired-end sequencing [high quality](https://github.com/ga4gh/quality-control-wgs/blob/0290612d0237078dea7ae38dc13…
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### Project short name:
RegenerativeLineagesLungMetastasis
### Primary Wrangler:
Ida
### Secondary Wrangler:
Arsenios
### Associated files
* Google Drive: [folder](https://drive.google.com/drive/f…
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I want to look at alternative splicing. My gtf has both gene name and transcript names that make this possible. I was wondering if there's a way to pull this information per cluster using seurat and…
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I tested a read pair that both R1 and R2 are exactly reverse complement. This sequence has multiple copies in the reference genome. When mapped the read, strobealign return a paired of location that n…
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thank you for developing this nice aligner. I was wondering what is the recommended range of query length for MA? Can it be used to align assembled contigs with length up to 10M bases to the reference…
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I only saw the protocol for integration of assembled subreads from PacBio ccs sequencing in combination with short read Illumina RNA-Seq and protein database, i don't know whether it can works with …
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Hi, Dr. Yang.
The canvasPainter.py code in DeepMosaic:
Line 38, maybe should replace 'offset = 0' using 'offset = int(start-start_pos)'
Because a deletion may occur which will lead to 'start !…