User: st.ph.n
st.ph.n • 990
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Posts by st.ph.n
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... what do your ids look like in your fasta? If they have similar patterns, such as different isoforms from Trinity for example, where you want to the longest isoform per gene cluster, I have a scrip that may help. ...
written 1 day ago by
st.ph.n • 990
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Comment:
C: processing FASTA file
... Why did you tag R? Others have given some viable options, but you didn't post anything that you had tried using R (i.e. code snippet), or that you *need* to use R. This would be easy with Biopython. ...
written 1 day ago by
st.ph.n • 990
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... This would work if the fasta was a single-line fasta and not multi-line like the OP has. ...
written 1 day ago by
st.ph.n • 990
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... Can you post the error message?
Make sure `file_1.txt` is tab-delimited, and doesn't have spaces.
> When I printed out the "seqs" part, I found out that the sequences
> were not complete
Did you linearize your fasta?
Is this homework? If so, and you were instructed to use Biopython, you ...
written 1 day ago by
st.ph.n • 990
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... Thanks for the tips, Matt. I should learn more about pyfaidx. Having a single-line fasta to work with is just a preference of mine, otherwise I would read the file in with Biopython. I like also to write parts out so the OP can learn something and understand what's going on, and without knowing the ...
written 3 days ago by
st.ph.n • 990
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... A Python solution. [Linearize][1] your fasta file, if it has more than one line per sequence. Save this code as `get_pos.py`. Change the names of `pos.txt` to your tab-delimited file, and `input.fasta` to the name of your fasta file. Run as python `get_pos.py > nucl_at_pos.txt`. `nucl_at_pos.txt` ...
written 3 days ago by
st.ph.n • 990
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... Yes, the sorted bam file. Snippet from the tutorial page, referenced above:
> Users must provide read alignments to Trinity as a coordinate-sorted
> bam file. Use GSNAP, TopHat, STAR or other favorite RNA-Seq read
> alignment tool to generate the bam file, and be sure it's coordinate
> ...
written 4 days ago by
st.ph.n • 990
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... You can provide the BAM file. I'm not sure if Trinity will complain if it is in SAM format. See [here][1] for tutorial. Make sure you sort you BAM/SAM file with `samtools sort`
Ex.
Trinity --genome_guided_bam rnaseq.coordSorted.bam \
--genome_guided_max_intron 10000 \
...
written 5 days ago by
st.ph.n • 990
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... You might want to open a new question, and reference this one. ...
written 5 days ago by
st.ph.n • 990
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... What sequences are you blasting? Sounds more like you want a multi-sequence alignment. ...
written 8 days ago by
st.ph.n • 990
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