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- Containerize SRA toolkit
- Spot check several SRA datasets for packaging formats (get access?)
- Modify pipeline to download SRA as input
- Start Azure boxes
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Hi,
I'm getting a lot of warnings like this:
> serialiser - orf.py:281 - WARNING - serialize - MainProcess - Invalid entry, reason: STRG.1000.1 not found in the index!
STRG.1000.1 0 3083 ID=STR…
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I'm trying to run junctionseq to look at the alternative splicing between two subgenomes in a tetraploid but I've run into a number of issues.
First, the number of annotated exons (or, at least th…
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I manually inspected the top isoforms and I think I could have found a major bug in RSEM.
Consider a particular transcript quantitated in two samples. In the first sample, RSEM estimates 0 counts.
…
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We've only seen this error when running MatrixEQTL on the exon-exon splice junction matrix. All of the junctions are sorted
```
2018-01-25 14:16:09 running MatrixEQTL
Matching data files and lo…
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Three particular cases of the Lexogen SIRV synthetic RNA spike in (ground truth, so every mapping junction has the correct answer) have different - and now incorrect - mapped junctions after switching…
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Hi Heng,
I'm not clear how minimap2 is functioning in terms of identifying splice sites. Given that the sequence reads may contain base miscall and/or indel type errors, it seems likely that splice…
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Output sam files from the STARlong aligner contain two custom tags (jM and jI) that describe whether each splice junction is canonical and where each intron begins and ends. TranscriptClean uses these…
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Hello,
Can we use minimap2 on 1D2 data from albacore?
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Hi, I have scRNAseq data with cell barcode and UMI in the Barcode read and and an additional plate barcode at the end of the cDNA read. I can extract the plate barcode from the cDNA read in a preproce…