User: gtasource

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gtasource20
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Posts by gtasource

<prev • 29 results • page 1 of 3 • next >
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Comment: C: Finding if Sequence is Present in Long List of Other Sequences from Multiple Spe
... 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 gtasource20
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Comment: C: Finding if Sequence is Present in Long List of Other Sequences from Multiple Spe
... 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 gtasource20
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Comment: C: Finding if Sequence is Present in Long List of Other Sequences from Multiple Spe
... 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 gtasource20
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Finding if Sequence is Present in Long List of Other Sequences from Multiple Species
... 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 ...
sequence search sequence alignment written 1 day ago by gtasource20
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Comment: C: Turning a Reference Genome Into a File With Single Nucleotide Positions (Essenti
... 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 gtasource20
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Comment: 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 gtasource20
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Comment: 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 gtasource20
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Comment: 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 gtasource20
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logCPM to RPKM
... 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 ...
rna-seq written 7 weeks ago by gtasource20 • updated 7 weeks ago by Devon Ryan84k
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Comment: 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 gtasource20

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