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Recent Replies
Comment: zero TPM for many gene including housekeeping when using kallisto
by
ATpoint
82k
Yes, but this is what I am saying: GAPDH in human has at least 6 annotated transcripts. Have you looked at all of them? Maybe that particul…
Comment: zero TPM for many gene including housekeeping when using kallisto
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ashkan
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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 …
Comment: zero TPM for many gene including housekeeping when using kallisto
by
ashkan
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@dariober: I have to use kallisto for our downstream pipeline.
Comment: zero TPM for many gene including housekeeping when using kallisto
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ATpoint
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Which celltype is this? Are these transcripts of the same gene, and of which gene?
Comment: zero TPM for many gene including housekeeping when using kallisto
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ashkan
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@atpoint the question is updated. the first command shows how the index is built.
Comment: Help! Reconstruction of locus, order contigs
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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.
Answer: In one PCA plot, can I calculate the percentage of different factors that contri
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diqixiaoyaoer
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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).
# …
Comment: Details on salmon index
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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…
Comment: What marks a De-Novo Genome assembly as FAILED?
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I'm a little confused about your experimental design. Are you making 45 different assemblies? Or are all the samples from the same individu…
Comment: zero TPM for many gene including housekeeping when using kallisto
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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 …
Comment: zero TPM for many gene including housekeeping when using kallisto
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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
Based on the error it appears that the input file you are providing could not …
Answer: How to handle duplicated genes in TCGA data?
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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…
Comment: Merge clusters in Seurat UMAP
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kilcdincer
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It did not help either. But I got the answer [here][1]
Thank you!
[1]: https://github.com/satijalab/seurat/issues/8902
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