User: mforthman
mforthman • 30
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Posts by mforthman
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... actually, I need to make it 'append' (>>) to the output file or else it just overwrites the output file with the last set of exons it concatenated. ...
written 8 weeks ago by
mforthman • 30
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... Thanks Pierre for the recommended commands. I tried to use it, adding a command to direct output to a new file, but it resulted in an empty file. Without that included, it prints sequences it concatenates to the screen (it does not print sequences that do not get concatenated with anything else). Pe ...
written 8 weeks ago by
mforthman • 30
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... I have a single fasta file with multiple exons from various genes. What I would like to do is use the GeneID in each header to find those exon sequences that have the same GeneID and concatenate them into a single sequence. Along with this, I would like to alter the sequence header so that it includ ...
written 8 weeks ago by
mforthman • 30
• updated
8 weeks ago by
Pierre Lindenbaum ♦ 124k
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... This was great! After some time trying to sort the file, I think I got bedtools to do exactly what I wanted with the .gff file. Next step is to figure out how I can use the bedtools output to extract the "new" exons (what I'm more interested in for downstream analyses) from the corresponding NCBI ge ...
written 8 weeks ago by
mforthman • 30
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... For a given gene, I would like to take the exons or CDS coordinates for all isoforms and 'merge' them to create a reference transcript that represents the 'maximal' number of coding regions. I have seen some previous posts that address this issue, but they only apply to Swiss-Prot, Entrez, Ensembl, ...
written 8 weeks ago by
mforthman • 30
• updated
8 weeks ago by
Brice Sarver • 3.2k
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... Running fastq-generated SRA files from NCBI through prinseq-lite. The program generates an error:
Use of uninitialized value $qual in scalar chomp at /apps/prinseq/0.20.4/bin/prinseq-lite.pl line 2583, line 26875674.
It still continues on until it has finished, but clearly there is somethin ...
written 19 months ago by
mforthman • 30
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... I have been trying to download SRA data from NCBI and putting it in fastq format using fastq-dump. A colleague and I have been trying to figure out why the resulting fastq files are causing some errors when inputted into prinseq-lite.
My collaborator has been using this fastq-dump command:
fas ...
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... I've still been tinkering with the script and feel as though I might be getting closer to the solution:
#!/usr/bin/env python
import sys
import re
original_fn = sys.argv[1]
company_fn = sys.argv[2]
pattern = '(uce.+$|ENSOFAS.+$|[AB]_[0-9]+$)'
map = {} ...
written 2.1 years ago by
mforthman • 30
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... You are correct, that was my mistake. Thanks for catching that! And I appreciate you taking a further look at this later. ...
written 2.1 years ago by
mforthman • 30
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... Correct, I kept the original question simple in original post. In reality, the company.fasta file had many differently formatted headers. I used the script you had provided to process just the `uce` headers, which worked. I already had the `ENSOFAS` headers. This leaves the others to be formatted. T ...
written 2.1 years ago by
mforthman • 30
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