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Comment: zero TPM for many gene including housekeeping when using kallisto
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@atpoint these are from PBMC. no they are different genes. for example ENST00000229239.10 is GAPDH. in STAR I got a lot of reads aligned …
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@dariober: I have to use kallisto for our downstream pipeline.
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Which celltype is this? Are these transcripts of the same gene, and of which gene?
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@atpoint the question is updated. the first command shows how the index is built.
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Is the *de novo* annotation required for each contig? Reconstructing homologous regions in many genomes can be tricky regardless, but is es…
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You can have a look on my answer. I have post it below.
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Here is my script that can be used to calculate how much degree that different factors contribute to PCA variance (PC1 and PC2).
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Thank you so much for the beautiful explanation. Just one more curiosity. So in the first versions Salmon utilized RapMap to index and then…
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You should be stating how you constructed the index, and include the actual lines for the problematic genes from the abundance files. Note …
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You could try [salmon](https://combine-lab.github.io/salmon/getting_started/) to see if the problem is with kallisto or with the pseudo-ali…
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> INPUT FILE error: could not open input file /geneInfo.tab
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Having duplicate gene symbols is pretty common. Why do you need to work with gene symbols? To compare them to external datasets? Or just fo…
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It did not help either. But I got the answer [here][1]
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there is no `--allsample` option in the "usage" screen you're showing. I suspect you're using an old version ?
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