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GFF files normally get converted to GTFs for the alignment pipelines, but for pseudoalignment, the gffs don't get converted:
```
nextflow run czbiohub/rnaseq \
-r olgabot/merged-salm…
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Hi,
Running a mixed species (mouse+human) 10x sample, RNA-seq v3. I am following the mixed species ipynb example: https://colab.research.google.com/github/pachterlab/kallistobustools/blob/master/no…
mliiv updated
4 years ago
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We can consider adding pseudoalignment approaches (Kallisto/Salmon) for comparison with aligners, but since these approaches rely on transcriptome it makes little sense to do a transcriptome-based rea…
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Hi, just tried running the loompy from fastq using the tutorial files. Everything ran fine up to the last step. I tried uninstalling and reinstalling h5py per suggestions from similar errors on stack …
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I suspect this might be a concurrency bug.
I have a pair of fastq files with 137,592,951 reads. I verify the number of reads using `wc -l`:
```
$ gzip -dc /Users/stelin/kallisto_GRCh38/HL73JBC…
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Hi,
I'm getting a 'resource temporarily unavailable' error when trying to write the bam pseudoalignments file in single-end mode. It's weird since I'm running hundreds of samples in batch and about …
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Hi, pseudoalignments are an interesting application for metagenomics. However I failed to build a database based on the current bacterial NCBI refseq database. Here is the output:
```
time kallisto …
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Would it be possible to output a pseudobam file, similar to kallisto?
We'd use the pseudobam file to clean PCR duplicates by using unique molecular identifiers (UMI), often used when doing single-cel…
roryk updated
5 years ago
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Hi,
I am currently dealing with a version of Smart-Seq2 data which is 150x150bp and has, on read 2, positions 1-8 as the cellular barcode and positions 9-16 as the UMI. For pseudoalignment with kal…
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A few updates for the SOP:
- [x] Add Best Practices reference (and possibly Fig1)
- [x] Require both methods for the exercise
- [x] Update intro section to emphasize building up knowledge and bac…