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Hi,
I wanted to confirm that we are calculating the saturation rate correctly for our CITE-seq data. We have a run_report.yaml output as follows:
Date: 2020-10-29
Running time: 4.0 hours, 43.0 minu…
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Hello,
Great package. However, I am running into an issue when loading in my files with RepLoad. Specifically, my files are filtered_contig_annotation.csv files from 10X. However, these are the onl…
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## Need
Related to this issue: https://github.com/Clinical-Genomics/BALSAMIC/issues/1282
Optical duplicates have not been detected and traced in the TGA workflow due to the presence of UMI tags …
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Hi,
I'm investigating this software as a faster alternative to umi-tools, but our pipeline already extracts UMIs into the `RX` sam tag. Umi-tools can handle this with `--extract-umi-method tag --u…
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I could not find description about how deduplication is done for fastq with UMI. I found "fastp considers one read as duplicated only if its all base pairs are identical as another one." Is it the sam…
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Hello,
Would it be possible to create 1000s of per-cell fast{q,a}s (preferred) or per-cell bams from the mega-bam of the 10x channel run? We wrote a tool to do this in Python, but it is slow and take…
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Hello,
I'll be soon getting data RNA-seq data with UMIs, and I was interested in running pair consensus decoding on the data. I noticed the paper's and bonito's implementation takes the reverse com…
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In order to allow wider adoption of the UMI-tools deduplication methods beyond simple position + UMI based deduping we would like to create a C library that implemented the core algos.
As much as p…
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1) spend more time on last 3 days and less on processing raw reads
differential isoform analysis?
minimum # reads per cell
umi-counting with kallisto how to aggregate umis from transcripts to genes…
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Hi,
I was worried about what exactly represents the output of 'Number of unique reads' in collapsing reads from fastq?
Number of input read 6609696
Number of unique reads 3885326
Number of reads …