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Recent Replies
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 th…
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
•
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'…
Comment: 18S taxonomy assignment SILVA database formatting
by
antonioggsousa
2.9k
Please, whenever you need to add more information, just edit your original post and do not add answers below unless you found the solution …
Comment: Clustalo failing to complete multiple sequence alignments
by
saamhasan55
▴
10
Hi, I know this is an old thread, but I am encountering a similar problem. I am trying to do an msa for the cds sequences of 5 bumblebee sp…
Comment: 18S taxonomy assignment SILVA database formatting
by
antonioggsousa
2.9k
Hi!
Please share first with us an example how the data looks like, the command-line you're running and the problem that you're getting. If…
Answer: Finding sequences in unannotated genomes using reference coordinates
by
Prangan
▴
20
I may have stumbled on a solution for this problem. What I wanted was the SNPs or mutations in the VCF to be incorporated in the reference.…
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