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Hi, first of all thanks a lot for this incredibly useful repository.
I am following GTEx v9 (using the branch, because v8 run_rnaseqc.py gives me 0 counts for all exons/transcripts/genes) pipeline …
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Hi, thank you very much for developing zUMIs!
**Describe the bug**
I have ~ 4,000 genes (introns+exons) in my zUMIs single-cell count matrices. However, while running velocyto (Velocyto: yes), I c…
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I am trying to use _tximeta_ (1.4.3) to import read counts from _alevin_ (1.1.0) using a custom annotation (Ensembl + technical sequences) and a decoy-aware transcriptome.
I am able to make the lin…
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Hi,
A very useful feature in ORFik is collapsing duplicated reads, adding scores according to count, and weighed coverage calculation with coveragePerTiling (or rather coverageByTranscriptW).
I foun…
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Hello,
I keep getting stuck at the TE index build, for both TEcount and TEtranscripts commands.
I've tried to use the curated GRCh38_rmsk_TE.gtf:
`1 hg38_rmsk exon 10469 11447 3612 - . gene_i…
alp78 updated
4 years ago
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Hello I have a problem in reference building
![Uploading Screen Shot 2020-09-19 at 18.45.31.png…]()
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When downloading the data from TSVdb, what are the units of the exon usage value, and how can I get RSEM values from those?
Thanks
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Running on a single (SE) FASTQ file as in the manual fails (it fails the same, as far as I can tell, on a pre-built BAM):
```
roylab@trypsin /mnt/trypsin_extra/no_backup/glarue/physarum/physarum_ext…
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Hi,
Is there a way for DGE to output the counts of the individual transcripts of every gene instead of the gene level counts? Since the summary file contains a column with NUM_TRANSCRIPTS, I assume t…
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Hello,
I've used Kallisto for quantification and rather than building my own Kallisto index I downloaded the one they provide for mm10 from here:
https://github.com/pachterlab/kallisto-transcri…