User: tshtatland
tshtatland • 60
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Posts by tshtatland
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1
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268
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... Use this perl one-liner:
echo ">BNY.1.2.t17987.mrna1 CDS=1-1065\nACTG" | \
perl -lpe '
s{\s.*}{};
s{[.][^.]+\z}{};
'
In the example based on the header you showed, it prints:
>BNY.1.2.t17987
ACTG
Here, these command line flags are used:
`-e`: tells the Perl ...
written 8 months ago by
tshtatland • 60
1
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1
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256
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1
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... Use variant allele fractions to detect contamination. See, for example:
*Same-Species Contamination Detection with Variant Calling Information from Next Generation Sequencing.
Tao Jiang, Martin Buchkovich, Alison Motsinger-Reif,
bioRxiv 531558; doi: https://doi.org/10.1101/531558*
*Posted Janu ...
written 9 months ago by
tshtatland • 60
0
votes
1
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251
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... The rest of the normalization should be done as recommended in the metagenomics packages, which I assume depends on the package. Additional normalization for gene length using TPM, for example, still makes sense, even if you first downsample to the same number of reads. ...
written 9 months ago by
tshtatland • 60
0
votes
1
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251
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1
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... I suggest to downsample all fastq files to the same number of reads prior to the analysis. This is a method commonly used in many other applications, such as RNA-seq and variant calling. ...
written 9 months ago by
tshtatland • 60
2
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2
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857
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2
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Answer:
A: Edit score column in bed file
... My preferred choice is to write the regions as a bed file from your code (python, etc). Then use standard bioinformatics tools, here `bedtools intersect` with option `-loj` (Left outer join. Report features in A with and without overlaps. See: [https://bedtools.readthedocs.io/en/latest/content/tools ...
written 18 months ago by
tshtatland • 60
2
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1
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934
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... A private installation of Biostar-like site would be similar in spirit to a private or local installation of any other tool, and of course it would require customization (and maintenance, hence the question). Only internal users can change or view the content. The content discussed there is specific ...
written 3.1 years ago by
tshtatland • 60
4
votes
1
answer
934
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1
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... Does anyone have experience installing and maintaining Biostar or a similar Q&A platform in-house (private, not open to public)? We are looking for a Q&A web application, suitable for low traffic, less than 1000 users, with varying computer skills. Any advice or recommendations are appreciat ...
written 3.1 years ago by
tshtatland • 60
• updated
3.1 years ago by
Jean-Karim Heriche ♦ 23k
0
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3
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4.1k
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... See the answer from Vijay Lakhujani above. More specifically, remove whitespace from the fasta reference **sequences** (whitespace in fasta header is okay). See also:
Burrows-Wheeler Aligner / Mailing Lists
https://sourceforge.net/p/bio-bwa/mailman/message/33230220/
https://sourceforge.net/p/bio-b ...
written 3.3 years ago by
tshtatland • 60
Latest awards to tshtatland
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8 months ago,
created an answer that has been accepted.
For A: Edit score column in bed file
Scholar
18 months ago,
created an answer that has been accepted.
For A: Edit score column in bed file
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