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Hello,
I could use your help troubleshooting this! Thank you so much!
****THE COMMAND I RAN FOR QC:****
`sqanti3_qc.py m64345e_220712_195752.gff genes.gtf GCA_000001405.15_GRCh38_no_alt_analys…
ghost updated
5 months ago
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[update]: oops, I just realized you can use `kallisto quant-tcc` to do this
I know there are workarounds for this but it would be nice to have a `--transcript-counts` option for `bustools count` th…
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- [x] fix excessive # of genes
- [x] fix out of order isoforms
- [ ] fix bad gene count (1400, should be 42K)
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From apollo-performance code
```
grep "WormBase\tgene\t" loaded-data/worm/…
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Do you recommend any tool to annotate 5'UTR, CDS, 3UTR features in the isoforms generated from `FLAIR`
akk01 updated
2 years ago
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Hi Vadim,
I’ve been running into this issue, raw files acquired from Orbitrap Astral are not loaded by Diann, no matter it’s 1.8 or 1.9 version/1.9.1 of diann. It happens occasionally, not for all …
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Genome based transcriptome assemblers like Cuflinks produce large no of transfrags. Are these real? if not, they are likely to impair differential expression analysis of isoforms adding more confusion…
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Hi, I aligned the transcript to the reference genome, and based on the coverage of reads, I found two alternative splicing events. However, the GTF file expanded by IsoQuant shows only one transcript …
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@nathanweeks in your example blast result I noticed that a lot of the hits for Tifrunner seemed to be different isoforms of the same gene. I am not %100 sure but I think current practice has been to u…
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I am trying the multisample mode, and running into out of memory issues which I expected to occur, but I can only assign a certain amount of RAM on my cluster. Is there a work-around for this.
So …