User: DVA
DVA • 490
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Posts by DVA
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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 8 weeks ago by
DVA • 490
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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 10 weeks ago by
DVA • 490
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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 11 weeks ago by
DVA • 490
• updated
11 weeks ago by
Devon Ryan ♦ 87k
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... Thanks for the help! Appreciate it. ...
written 4 months ago by
DVA • 490
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... Thank you very much! ...
written 4 months ago by
DVA • 490
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... Thank you for the comment @genomax, I am looking at individual base level. ...
written 4 months ago by
DVA • 490
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... Hello,
I wonder how to use a bam file to learn how many sites are not covered at all, how many are covered >=5 times and 20 times. We got such stats from our sequencing company, but want to see we can do it ourselves as well.
Thank you very much. ...
written 4 months ago by
DVA • 490
• updated
4 months ago by
Pierre Lindenbaum ♦ 116k
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... I am looking at somatic mutations across multiple samples, but the samples are not covered equally in many regions. Since we care about comparing the mutation counts between these samples, I would need to consider the uneven coverage -- e.g. sample A has 5X coverage at position 1, while sample B has ...
written 6 months ago by
DVA • 490
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