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Recent Replies
Comment: NGS forensics: how to know if data is fabricated
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> 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…
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If you have independent information available (e.g. genotype data for both samples) then you *may* be able to assign reads based on the pre…
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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?
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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
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salias
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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
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> 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
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salias
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Following your advice, I checked the primer and adapters sequences and edited the question accordingly
Comment: How should I make kallisto indexes?
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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?
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"./." in your gVCF files typically indicates a lack of information or uncertainty about the genotype at that particular position.
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Fungal ITS2 region (length is really variable so read-through can be an issue)
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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
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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
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salias
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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?
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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
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> 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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