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Recent Replies
Comment: STAR aligner.. Are reads checked against each chromosome sequentially?
by
jv
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160
> I'm new to bioinformatics
All the more reason why it is important that you do your homework and dig into the literature. There are count…
Answer: Which is the file containing genome assembly?
by
cfos4698
▴
460
All of the provided files are explained in the README.txt file (https://ftp.ncbi.nlm.nih.gov/genomes/genbank/vertebrate_mammalian/Acinonyx_…
Comment: Saccharomyces cerevisiae TFs
by
jv
▴
160
I agree with @lievensterck - that said, you might want to take a look at what is available via the JASPAR REST API <https://jaspar.genereg.…
Comment: Map a list of gene names in UniProt
by
jv
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160
First, I think there is some confusion. Your gene names are not accession ids which is what I was inquiring about in my first question. Wha…
Answer: Technical replicates in Microarray data
by
Gordon Smyth
★
3.9k
The best way to handle technical replicates often depends on the context and the overall experimental design, which you haven't told us muc…
Comment: How do I access pymol alignment object ("object=" arg of align function ) from p
by
Wayne
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670
In your python version of the code (for the PyMOL API), try adding double-quotes (since you use single quotes already on those lines) aroun…
Comment: How does Cellranger handle different versions of the same gene?
by
markddesimone
▴
50
@rpolicastro thank you for that. Unfortunately, the data I have (which was downloaded from https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?a…
Comment: Does anyone have experience making custom references for 10X Genomics' cellrange
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chrisblazier
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0
Thanks, I have contacted them and they have been helpful. Unfortunately they really don't have experience outside of human and mouse, so pr…
Comment: MultiProcessing on SeqIO biopython
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Wayne
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670
It should be pretty easy to test this? How slow is it without parallelization with a few of the average size chromosomes you have available…
Answer: Spatial transcriptomics without the h5 file
by
matt_hias
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0
Hey jordi,
I didn't find a method to directly write the sparse matrix into a .h5 file. But as workaround you can store the raw values in a…
Comment: How to generate Artemis ACT comparison file?
by
lieven.sterck
13k
you should have done a search first ;-) ...
https://www.biostars.org/p/142951/
Comment: Saccharomyces cerevisiae TFs
by
lieven.sterck
13k
you might want to consider elaborating on what you consider "a list" . Perhaps add some dummy example?
Comment: Why there are symmetric splice junctions on IGV?
by
Apex92
▴
80
Thank you Jeremy for giving input - I looked at my bam files, my reads are unstranded (I thought they were stranded).
Comment: DESeq2 modelling and Wald's test
by
FantasticAI
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60
Hi Kelvin, I have a question related to DESeq2 modeling and test too. In my case, I have two groups (6 samples for each group). I can get 1…
Comment: Why there are symmetric splice junctions on IGV?
by
Jeremy Leipzig
20k
you need to look at **one** gene - any gene - to see if it's stranded or unstranded
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