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Recent Replies
Comment: Check barcode collision
by
Vincent Laufer
★
2.4k
https://satijalab.org/seurat/reference/read10x
yes there is a specific function called read10x aimed at this sort of thing :-D
Answer: Tool for extracting part of aligned sequence by CIGAR string
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cmdcolin
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this does not necessarily answer your question, but becoming familiar with parsing CIGAR is sometimes quite useful
Here is a short code th…
Comment: Error in converting vcf file to plink format
by
Madhawa
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Hi,
I have another issue when I work with this data set. After I obtain the BED, BIM and FAM files, I tried to do some QC steps for this d…
Answer: Create the design matrix for limma differential expression analysis.
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Gordon Smyth
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See
[A guide to creating design matrices for gene expression experiments](https://bioconductor.org/packages/release/workflows/vignettes/RNA…
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> Normally they should be excluded from the analysis.
It will not mess up statistics or anything like that, but there will be no separat…
Comment: for loop and sapply for assigning name
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Untested since no example data was provided.
```
dfs <- lapply(list(df1, df2), \(x) {
colnames(x) <- info$name[which(info$id == colnames(…
Comment: Low alignment score for microRNA
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Just for the record. I did the conversion with
sed '/^[^>]/s/U/T/g' mature.fa > mature_conv.fa
to avoid modification of the header an…
Comment: Understanding bowtie2 for short reference sequences
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That was indeed my first approach, remove exact matches and then those with only substitutions (which are still relatively fast to identify…
Comment: Low alignment score for microRNA
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Since miRNA are small you will want to stick with an un-gapped aligner so `bowtie v.1.x` is a fine choice.
Comment: Low alignment score for microRNA
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ntsopoul
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ok great I will try this. Maybe not in line with the thread but which aligner would you recommend to align the small-rna seq onto the genom…
Comment: Low alignment score for microRNA
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You could use `sed 's/U/T/g' mature.fa > conv.fa` as a quick brute force method. It may replace some `u` characters in fasta headers.
Answer: EDAseq, edgeR libraries cannot be installed in M2 mac
by
Gordon Smyth
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See https://stat.ethz.ch/pipermail/bioc-devel/2022-September/019178.html
PS. I'm curious why you don't sent such a Bioconductor-specific q…
Comment: EDAseq, edgeR libraries cannot be installed in M2 mac
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Can you install `samtools` via `conda`? That should include the `lzma.h` headers.
Comment: Low alignment score for microRNA
by
ntsopoul
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Oh thank you so much! This makes total sense…
So how dow I do the conversion and on which file? The mature.fa I guess …
Answer: Low alignment score for microRNA
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> Do I have to convert T to U?
Yes you have to do that conversion. Then align with a bowtie v.1.x index created after the conversion.
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