User: gtasource
gtasource • 20
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Posts by gtasource
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... Thank you jrj. I'm not extremely familiar with hidden markov model search methods. Do you have any additional resources I could look at? ...
written 1 day ago by
gtasource • 20
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... It's hard to say; since the 500nt sequence is from a different species, so I don't expect all of it to be intact. I was expecting more than just small (<20 nts) matches however.
"Somewhat similar sequences" is a setting you can select when you are doing a BLAST. ...
written 1 day ago by
gtasource • 20
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... Thank you for the reply. Unfortunately, we the sequence of interest is an enhancer region, so there are no protein level comparisons available. ...
written 1 day ago by
gtasource • 20
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... Hello,
I have a sequence of 500nt, that has an important function in Species X. I have a list of about 20 other species, with coordinates of about ~20,000, that I want to see if they contain this important 500nt region. I did an initial BLASTN between this sequence and the 20 other sequences, and ...
written 1 day ago by
gtasource • 20
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... The reference fasta is separated by chromosomes. Here's what I was thinking of doing: What I was planning on doing was to create a bed file based upon the chrosomes, and then expand the file for every single nucleotide. Only issue is I want to know what the reference genome nucleotide is at every ...
written 7 weeks ago by
gtasource • 20
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C: logCPM to RPKM
... Thanks so much. I realized the data that was labeled as logCPM wasn't accurate. I went ahead and pulled the raw count tables, and calculated everything manually. Thanks for your help! ...
written 7 weeks ago by
gtasource • 20
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C: logCPM to RPKM
... I did! Thanks, I appreciate it. I should also note that these logCPM values are coming directly from edgeR! ...
written 7 weeks ago by
gtasource • 20
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C: logCPM to RPKM
... Kevin, I completely agree with you. However, a collaborator I am working with has specifically asked for RPKM values. I do believe they also understand the limits of using it compared to logCPM, ect. ...
written 7 weeks ago by
gtasource • 20
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... I have logCPM values I'm trying to convert to RPKM. Doing a search, I found you can convert it by doing the following:
RPKM = 2^(logCPM-log2(geneLength))
However, this is giving me negative RPKM values, as most of the gene lengths in log2 form are larger than the logCPM values (unless my math ...
written 7 weeks ago by
gtasource • 20
• updated
7 weeks ago by
Devon Ryan ♦ 84k
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C: Introns from Exons of GTF File
... Thanks! Im still getting the "exceeds the length of chromosome." Do you think I should change it from 0 to 39238 to 1 to 39238. Or even subtract one from the sizes? Kind of confused as to why it's saying it's exceeding the length. ...
written 8 weeks ago by
gtasource • 20
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