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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
Comment: samtools tview symbols
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Recent Replies
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 …
Comment: Too many unpaired forward reads found by Trimmomatic
by
SilhouetteQ
• 0
Using fastp, I found that the adapter sequence for the forward read is corresponding to Trans2_rc in the NexteraPE-PE.fa, while for the re…
Comment: cellranger error message
by
Max
• 0
I think the problem is your fastq_id. This should also read "RabhiN_PHLGEX". Hope this helps!
Comment: How to format "I" and "D" in vcf version 4.2 for liftover analysis in GATK
by
Giulio Genovese
▴ 400
@yokofakun is correct. Also, do notice that the GATK option `--RECOVER_SWAPPED_REF_ALT True` does not work with indels. In general, if your…
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