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Comment: Extract Loci based on the snps number
by
Yogi
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40
I think this may be what you're looking for.
You can subset by regions.
https://samtools.github.io/bcftools/bcftools.html#view
Comment: Kraken2 is falsely assigning Klebsiella
by
SushiRoll
▴
110
Hi Philipp,
Thanks for your feedback. I found that 0.1 outputs includes most of the species the authors claim to be in their mock datase…
Answer: Filter vcf SNPs by sample GT value
by
Pierre Lindenbaum
157k
with GATK selectVariant https://gatk.broadinstitute.org/hc/en-us/articles/360037055952-SelectVariants a **JEXL** select expression (not te…
Answer: tximport error: vroom
by
Trivas
★
1.5k
Which version of Salmon are you using? According to the `tximport` documentation, older versions of `quant.sf` files from Salmon have comme…
Comment: Need help to setup a PGS pipeline
by
GenoMax
135k
You will need to provide at least one way for people to contact you. Please edit the post and add that information.
Answer: Kraken2 is falsely assigning Klebsiella
by
Philipp Bayer
7.9k
I've also had false positive hits with Kraken, usually a --confidence of 0.1 gets rid of *most* of them.
This paper deals a bit with the …
Comment: Rockhoppper - Suspiciously low percentage of perfectly aligned reads
by
langziv
▴
50
I reduced the data to 50x with seqtk and got the same percentage.
What do you think about combining the assembly so that it will be a gen…
Comment: 18S taxonomy assignment SILVA database formatting
by
GenoMax
135k
https://www.biostars.org/u/96c44ed8/ : Please take a moment to properly format the original post. Highlighting text and then using `101010`…
Comment: 18S taxonomy assignment SILVA database formatting
by
mbuenner
•
0
To me it seems consistent in the fungi. I will filter for the Fungi.
So you helped me a lot actually! Thank you!
Comment: tximport error: vroom
by
Kevin Blighe
86k
Cross-posted: https://support.bioconductor.org/p/9154550/
Comment: 18S taxonomy assignment SILVA database formatting
by
antonioggsousa
2.9k
I understand the issue, but I do not have an easy fix.
The problem is that some sequences have different levels of taxonomic levels. For …
Comment: Error in checkFullRank(modelMatrix) :
by
Basti
★
1.7k
Apart from the response below, your design is strange. Why did you want to adjust for sample if you want to compare the expression between …
Comment: 18S taxonomy assignment SILVA database formatting
by
mbuenner
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0
Changing it a bit to
`$ awk 'BEGIN{FS=";"; OFS=";"} /^>/ { print $4,$5,$6,$7,$8;$9;$10; next; }; { print; }' SILVA_132_taxonomy_assignmen…
Answer: 18S taxonomy assignment SILVA database formatting
by
antonioggsousa
2.9k
I'm not an expert on `awk`, but I tried the following and it seems to work. Instead of using the original downloaded file, give your latest…
Comment: 18S taxonomy assignment SILVA database formatting
by
mbuenner
•
0
Thank you for editing the post and for your answer.
Sadly, the linked formatted database does not contain Fungi, e.g. when I grep 'Fungi'…
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