User: DVA
DVA • 530
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Posts by DVA
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... I have been using Monocole2 to study the progression of cells into a disease state and have had good results clustering the cells, identifying deferentially expressed genes, and plotting a pseudotime continuum.
However, I would also like to identify genes that are critical to the initial transitio ...
written 4 months ago by
DVA • 530
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... Hello,
I am interested in a small domain of a well studied and well defined protein (Huntingtin), and would like to see how conserved this domain is across species. In particular, I would like to address two questions in a scientific (publishable) way:
How well conserved across species is this do ...
written 11 months ago by
DVA • 530
• updated
11 months ago by
Bill Pearson • 860
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... Thanks so much! I appreciate your help. ...
written 11 months ago by
DVA • 530
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... Hello,
I hope this question is not too silly. What would happen to SNVs callers such as GATK, if a region has some kind of structure variations? Would the caller be able to tell?
Thank you! ...
written 12 months ago by
DVA • 530
• updated
12 months ago by
WouterDeCoster ♦ 43k
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... Hello,
Does anyone have a protocol or recommended pipeline for doing differential peak/binding analysis in Partek. I want to compare ATAC-seq results from two different conditions, but a ChIP-seq based pipeline would also be useful.
Diffbind and csaw seem good but these are not available in Parte ...
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... Could you please recommend me a database where I can get gene expression pathway data? Essentially, this database should have information along the lines of "expression of X causes an increase/decrease in the expression of Y".
I am studying RNA-seq data and information about "protein X binds prote ...
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... Hi @JC, thanks a lot for the reply! This is an interesting point - for the human case, it falls at the end with only one of the isoforms it seems like. I guess to use this design, that would require a very thorough annotation. ...
written 15 months ago by
DVA • 530
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... Hello,
I have a few 3' RNA sequencing data sets that have mixed human and mouse samples. As I am trying to split these reads apart, during the alignment (transcript region only) step, I noticed that there are about 3-5% of reads that can be mapped to both references - with VERY similar map-able bas ...
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... Thank you for the conformation. I will update this post once I hear from them. ...
written 15 months ago by
DVA • 530
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... Hello,
I am trying to understand an error when running "samtools view":
Line 6040, sequence length 67 vs 76 from CIGAR
Parse error at line 6040: CIGAR and sequence length are inconsistent
I went back to check line 6040 from sam file (generated by HISAT2):
NR500449:117:H7WMXX:2:11101: ...
written 15 months ago by
DVA • 530
• updated
15 months ago by
Devon Ryan ♦ 94k
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