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Recent Replies
Comment: Exonerate - issues when running it
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alex.zaccaron
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It doesn't look you are getting an error. I guess Exonerate is simply not able to map your protein sequences to your reference because ther…
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But the schematic seems to show a single consensus being called. Guess that is not correct? You did use the `subreads.bam` file as input, c…
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@genomax yes you will get the consensus sequence. that is in bam format. if you convert it to fasta you will see there are multiple entries…
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helloword
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Hi! I know it has been a long time but I cannot solve this issue. If you remember how to solve it, could you please help me? Compiling it a…
Comment: Pandas dataframe to H5ad file
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roy.granit
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880
Thanks, looks promising!
Meanwhile, I also came up with this:
# dataframe for annotating the observations
obs = pd.DataFrame()
…
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See if this helps in that case: https://chanzuckerberg.github.io/scRNA-python-workshop/preprocessing/00-tabula-muris.html
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helloword
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Hi, I am facing the exact issue. It has been 6.8 years but how did you fix this? Thanks in advance.
Comment: Pandas dataframe to H5ad file
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Thanks, I actually use sceasy for similar tasks, but was hoping to do this using python
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I converted the count matrix to seurat object (using `seurat` package) and then to h5ad. Library used is sceasy. However, it requires retic…
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Hi Shicheng,
Thank you. Sure, I will be glad to have a zoom call. Will email you.
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by
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137k
what is the output of
```
samtools view -H in.cram | grep '^@SQ' | grep -w chr1
```
and the output of
```
grep -w chr1 /path/to/referen…
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hi there. did you ever figure this out? i have the same problem
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gt
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actually, do you know how many freebayes uses for variant calling?
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I haven't done this in a while, but my recollection is that gnuplot file is a simple text with commands, which you should be able to modify…
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