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Comment: Truncated metadata file report from ENA Portal API
Comment: How to format "I" and "D" in vcf version 4.2 for liftover analysis in GATK
C: PLINK --score Erroe
Answer: PLINK Error: No valid entries in --score file.
C: PLINK Error: No valid entries in --score file.
Comment: Can I readmap short reads to rDNA references?
Answer: EdgeR - relationship between logFC and coefficients
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Recent Replies
Comment: extract viral protein of interest from 10k whole viral genomes
by
GenoMax
142k
With a large dataset it is always best to do the search locally (or in the cloud, if you don't have necessary hardware available locally).
Comment: Truncated metadata file report from ENA Portal API
by
Giulia
• 0
Thank you so much for your hint! I'll look into this!
Comment: How to convert Haps file to vcf file?
by
curious
▴ 750
unzip haps then: bin/shapeit \ -convert \ --input-haps {haps_prefix} \ --thread {cpus} \ --output-…
Comment: Can I readmap short reads to rDNA references?
by
aniigodwinn
• 0
Still on this, the reads are from org a, org b, and environmental contaminants. I have a fairly good idea what org b might be but i need to…
Comment: fastq screen aligner no specified.
by
Ximena
• 0
Thank u so much, my OS is linux. I will try your advice.
Comment: In IGV is this a heterogeneous mutation or false call?
by
Tuck898
• 0
No worries, I can completely appreciate that. I am having investigations similar to a condition causes by the RYR2 gene and was wondering i…
Comment: In IGV is this a heterogeneous mutation or false call?
by
Pierre Lindenbaum
161k
> RYR1 underneath although I was originally looking at the RYR2 gene. Sorry to sound stupid but does this make sense to what I've previousl…
Comment: In IGV is this a heterogeneous mutation or false call?
by
Tuck898
• 0
When click the blat it brings me to chr19 and mentions the RYR1 underneath although I was originally looking at the RYR2 gene. Sorry to sou…
Comment: In IGV is this a heterogeneous mutation or false call?
by
Tuck898
• 0
Thanks for that! I'll try and have a look and see what is amiss if I can... In your opinion what do you feel is wrong in my alignment from…
Comment: In IGV is this a heterogeneous mutation or false call?
by
Pierre Lindenbaum
161k
yeah.. look at that, there is something wrong in your alignment, many reads were mapped in a location but they are all clipped, so somethin…
Comment: Custom Reference panel creation for data imputation from .vcf files
by
analyst
▴ 50
Hi [Kevin][1]! I have 80 samples of GBS data. I have called variants through GATK pipeline. Now I have to perform imputation. Do I need …
Comment: In IGV is this a heterogeneous mutation or false call?
by
Tuck898
• 0
Ah I've just found 'show soft clipped bases' and this is what comes up... how come it is all greyed out? ![enter image description here][…
Comment: In IGV is this a heterogeneous mutation or false call?
by
Tuck898
• 0
I've just displayed clipped bases and this is what it shows. Does this look right? ![enter image description here][1] ![enter imag…
Comment: In IGV is this a heterogeneous mutation or false call?
by
Tuck898
• 0
Hi, I really appreciate you taking the time to reply. I'm still learning with IGV and sorry to sound very inexperienced but how would I che…
Answer: In IGV is this a heterogeneous mutation or false call?
by
Pierre Lindenbaum
161k
there is a clear shift in the depth just close to this mutation, you should set IGV to display the clipped bases + check if there is a DUP …
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