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written 3 days ago by
Claire Watson
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written 4 days ago by
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written 6 days ago by
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written 8 days ago by
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updated 11 days ago by
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written 11 days ago by
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updated 11 days ago by
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15 days ago by
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updated 17 days ago by
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updated 18 days ago by
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written 18 days ago by
Transmitting Science communication
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19 days ago by
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written 19 days ago by
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written 21 days ago by
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updated 26 days ago by
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written 26 days ago by
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28 days ago by
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Recent Replies
Comment: NGS forensics: how to know if data is fabricated
by
noodle
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570
> Can you clarify what you mean by "100% of reads pass cutadapt, even
> though 70% of reads contain adapters and get trimmed.
The header o…
Comment: Software to separate reads from different individuals
by
GenoMax
141k
If you have independent information available (e.g. genotype data for both individuals) then you *may* be able to assign reads based on the…
Answer: Extract protein sequence
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Matthias Zepper
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You didn't mention what kind of organism you are working with and what kind of protein you are looking for?
If it happens to be a microbia…
Comment: How to use limma to find differentially expressed genes in response to a continu
by
pairedttest
▴
10
Thank you Gordon for your expertise. One question that I have now that I have a list of DE genes is how to interpret logFC of this continuo…
Comment: FastQC Quality per tile and per sequence behaving strange after using Cutadapt
by
salias
•
0
Yes I plan to use QIIME2, but I'm Cutadapting outside QIIME so its easier to MultiQC without importing/unzipping QZAs (and QIIME2 importing…
Comment: FastQC Quality per tile and per sequence behaving strange after using Cutadapt
by
GenoMax
141k
> 3' adapters were removed aprox. 90 times each one, so there sohuld not be read-through at all here
Then you have data that has poor Q sc…
Comment: FastQC Quality per tile and per sequence behaving strange after using Cutadapt
by
salias
•
0
Following your advice, I checked the primer and adapters sequences and edited the question accordingly
Comment: How should I make kallisto indexes?
by
dsull
★
5.9k
We can't phase them out per se, because ``kallisto index`` is still the engine responsible for creating the index under the hood (and there…
Comment: When to use .vcf or .gvcf files from GATK HaplotypeCaller?
by
Medhat
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"./." in your gVCF files typically indicates a lack of information or uncertainty about the genotype at that particular position.
This co…
Comment: FastQC Quality per tile and per sequence behaving strange after using Cutadapt
by
salias
•
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Fungal ITS2 region (length is really variable so read-through can be an issue)
Answer: Is it possible to bulk download files from GEO repository?
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Also try the NCBI AWS bucket transfer tool. It's extremely convenient, however it's not instantaneous and you need to have a (paid) AWS acc…
Comment: FastQC Quality per tile and per sequence behaving strange after using Cutadapt
by
GenoMax
141k
Check a random sampling of reads to make sure the adapters are being removed. You may also want to blast a few reads to ensure that there i…
Comment: FastQC Quality per tile and per sequence behaving strange after using Cutadapt
by
salias
•
0
Many thanks for your comment. If read-through is happening, shouldn't Cutadapt being taking care of that there? I provided to the Cutadapt …
Comment: How should I make kallisto indexes?
by
bioinfo
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150
Thank you. I will read the documentation you attached. Are you going to slowly phase out the not kb ref commands? Also, does the t2g.txt fi…
Comment: FastQC Quality per tile and per sequence behaving strange after using Cutadapt
by
GenoMax
141k
> I need to understand why is this happening
More than likely you have library fragments that are shorter than the length of sequencing. W…
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