User: tshtatland

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tshtatland60
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60
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Location:
United States
Website:
http://ksvetu.blogspot...
Last seen:
3 weeks, 6 days ago
Joined:
4 years, 11 months ago
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Posts by tshtatland

<prev • 8 results • page 1 of 1 • next >
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Answer: A: Trimming of fasta file headers
... 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 tshtatland60
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Answer: A: How to check if a sample has been mixed with another sample based on NGS sequenc
... 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 tshtatland60
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Comment: C: Accounting for differences in FASTQ-file size, when comparing metagenomic gene a
... 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 tshtatland60
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Answer: A: Accounting for differences in FASTQ-file size, when comparing metagenomic gene a
... 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 tshtatland60
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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 tshtatland60
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Comment: C: Maintaning internal or private installation of Biostar or a similar Q&A site
... 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 tshtatland60
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Forum: Maintaning internal or private installation of Biostar or a similar Q&A site
... 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 ...
forum biostar written 3.1 years ago by tshtatland60 • updated 3.1 years ago by Jean-Karim Heriche23k
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Answer: A: BWA error [bns_restore_core] Parse error reading
... 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 tshtatland60

Latest awards to tshtatland

Supporter 5 weeks ago, voted at least 25 times.
Scholar 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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