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Recent Replies
Comment: dedup STAR transcriptome file using umi_tools
by
i.sudbery
20k
You should definitely be able to use samtools ti sort and then index the transcriptome bam. We've done this many times.
Comment: dedup STAR transcriptome file using umi_tools
by
Ar
★
1.1k
Yes, you are right. I plan to do this. Thanks!
Comment: dedup STAR transcriptome file using umi_tools
by
rfran010
★
1.3k
How about deduping based on the genomic bam, then filtering the transcriptome bam based on the reads leftover. Maybe some extra work, but m…
Comment: dedup STAR transcriptome file using umi_tools
by
Ar
★
1.1k
Yes, I am using the NEB's NEBNext UMI adaptors for the bulk RNA-seq samples.
Comment: dedup STAR transcriptome file using umi_tools
by
Ar
★
1.1k
Thanks for the reply. STAR generates two different bam files. One is the genome based and the other one is the transcriptome based. I am ab…
Comment: Are there any preferred trajectory/pseudotime analyses that do not require an ar
by
Jean-Karim Heriche
27k
Maybe consider seriation/ordination as an alternative.
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 …
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