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Recent Replies
Comment: dedup STAR transcriptome file using umi_tools
by
i.sudbery
20k
There are bulk protocols that include UMIs. Lexogen's CORRAL kits for example. Or NEB's NEBNext UMI adaptors.
Answer: dedup STAR transcriptome file using umi_tools
by
Michael
55k
I am quite sure that you cannot use UMI_tools to deduplicate bulk RNA-seq. The different oligo adapter sequences on each bead introduce UMI…
Answer: dedup STAR transcriptome file using umi_tools
by
i.sudbery
20k
I don't know if any reason you shouldn't be able to index the bam produced by STAR, although you will need to sort them first.
Comment: Compare Two Sigle-cell Sample for Differentially Expressed Genes (DEGs). How?
by
wangziwei0010
▴
30
Hi ATpoint,
Thank you for your though provoking answer. Big fans!
Actually I have some normal cells in each sample, and I found good mixt…
Answer: Differential binding analysis between different TFs
by
Ming Tommy Tang
★
4.5k
have you taken a look at csaw? https://bioconductor.org/books/release/csawBook/
also, I am not sure how you can compare different TFs, the…
Comment: R encountering fatal error and quitting the session
by
Dunois
★
2.7k
Have you tried running this in a fresh, clean `R` session with no other (unnecessary) packages and data being loaded into memory? How much …
Comment: PyDeseq2 - InvalidIndexError
by
Dunois
★
2.7k
You most likely have duplicates somewhere in there in the column that is currently serving as index to (I am guessing) the counts DataFrmae…
Comment: What to do with sequences without hits after doing blast against a reference tra
by
Dunois
★
2.7k
Expand your search by searching these (two) sequences against other sets of sequences.
That said, why does it feel like this is an [XY pro…
Comment: Compare Two Sigle-cell Sample for Differentially Expressed Genes (DEGs). How?
by
ATpoint
85k
It's confounded. SCtransform is not doing anything in such situations and hatmony operates on a per-cell embeddings level and not per gene …
Comment: count number of polymorphic sites among samples in vcf
by
vaellis
•
0
I'm wondering if this could work:
`bcftools query -f '[%GT]\n' my.vcf.gz | awk '{ gsub(/\./, ""); print }' | grep -Ev '^(.)\1+$' | wc -l`
…
Comment: GISTIC 2.0 parameter change not happening
by
Ram
44k
You should contact the [GenePattern google group](https://groups.google.com/g/genepattern-help) - that's where you stand a higher chance of…
Comment: find marker using scRNAseq data
by
allingt
•
0
What method are you using to identify markers and does it allow for nested designs?
Comment: count number of polymorphic sites among samples in vcf
by
vaellis
•
0
I will look into this. Thank you!
Comment: count number of polymorphic sites among samples in vcf
by
vaellis
•
0
example vcf:
```
CHROM POS ID REF ALT QUAL FILTER INFO FORMAT ind1 ind2 ind3 ind4
chr1 100 . C …
Comment: Snakemake expand(): using a helper function (zip) and imputing wildcards?
by
Jesse
▴
850
Not totally sure I'm right about your use case (are those config entries lists of strings, which is why you need to zip them?) but, you can…
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