User: athey.johnc

gravatar for athey.johnc
athey.johnc40
Reputation:
40
Status:
New User
Location:
United States
Last seen:
3 years, 3 months ago
Joined:
5 years, 1 month ago
Email:
a**********@gmail.com

Posts by athey.johnc

<prev • 11 results • page 1 of 2 • next >
0
votes
1
answer
1.3k
views
1
answers
Comment: C: TopHat Report Transcript Alignment
... I was actually advised by the bioinformatics office here, when I asked this same question of them, that using something other than tophat would probably require additional justification because it's still the standard. In any case, HISAT2 seems to have the same functionality and no clearly documente ...
written 3.6 years ago by athey.johnc40
0
votes
1
answer
1.3k
views
1
answers
Comment: C: TopHat Report Transcript Alignment
... Yes, I know-- what I meant was having to do it in two separate steps, the first time feeding it a "genome" containing each CDS as a separate entry, so that it would report the "genomic coordinates" as transcript alignments, and then take the unmapped.bam and run it through tophat again against the r ...
written 3.6 years ago by athey.johnc40
0
votes
1
answer
1.3k
views
1
answers
Comment: C: TopHat Report Transcript Alignment
... As mentioned, some of the reads in the sample are coming from unspliced mRNA containing introns, which won't align to just the transcriptome. I suppose it could perhaps be achieved by doing two separate alignments, first against the transcriptome, taking the unmapped reads from that and aligning the ...
written 3.6 years ago by athey.johnc40
2
votes
1
answer
1.3k
views
1
answer
TopHat Report Transcript Alignment
... I have a question that seems simple, but can't find an answer to anywhere: is there a way to make tophat, when aligning reads to a transcriptome and then genome, report the reads that are aligning to the transcriptome with transcript coordinates (in addition to genomic coordinates or on its own)? I ...
tophat alignment transcriptome written 3.6 years ago by athey.johnc40 • updated 3.6 years ago by Carlo Yague5.0k
0
votes
0
answers
1.5k
views
0
answers
GTF to FASTA including stop codon
... I am looking for a way to extract coding sequences, including their stop codons where available, using a genome and GTF annotations. None of the tools I've come across, including tophat's gtf_to_fasta and gffread, actually parse out the full sequence with the stop codon. Gffread has a flag -J, "disc ...
gtf fasta tophat gffread written 3.7 years ago by athey.johnc40
0
votes
2
answers
1.4k
views
2
answers
Comment: C: BLAST+ Collapsed Results
... Good to know. Thanks! ...
written 5.1 years ago by athey.johnc40
2
votes
2
answers
1.4k
views
2
answers
Answer: A: BLAST+ Collapsed Results
... In case anyone finds this in the future, with BLAST+ 2.2.31 that was released in June 2015, a new output format (outfmt 14), XML2, was released. Unlike the original XML output (outfmt 5), XML2 will properly split the hit ID/description tags, and most centrally to this question, each of these "collap ...
written 5.1 years ago by athey.johnc40
0
votes
1
answer
1.8k
views
1
answers
Comment: C: Reading CDS regions from a gbk file and counting amino acid codons in Biopython
... I'm not entirely sure what's causing the bug. People will include partial CDSs in their annotation, but in my experience, annotations are not very well standardized and the chances of running into malformed data can be high. If a CDS is partial, you may have to pay special attention to the /codon_st ...
written 5.1 years ago by athey.johnc40
1
vote
1
answer
1.8k
views
1
answers
Answer: A: Reading CDS regions from a gbk file and counting amino acid codons in Biopython
... I'm somewhat confused by your question, as I'm not sure which errors you're referring to in particular. 1) I believe the counts that you're seeing are different because the .count() method you're using on the concatenated string does not maintain the proper reading frame. The function is non-overla ...
written 5.2 years ago by athey.johnc40
0
votes
2
answers
1.4k
views
2
answers
Comment: C: BLAST+ Collapsed Results
... RefSeq is not actually that non-redundant. It's better than nr, which is why I'm using it, but there is significant overlap in a lot of sequences that is actually making my job a lot harder than it needs to be. See for example: NP_001171009.1, NP_001171010.1, NP_899245.1, as well as the other exampl ...
written 5.2 years ago by athey.johnc40

Latest awards to athey.johnc

Scholar 5.1 years ago, created an answer that has been accepted. For A: BLAST+ Collapsed Results

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2001 users visited in the last hour