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Pierre Lindenbaum
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Recent Replies
Comment: Normalization of RNA captureSeq data (<20 genes captured)
by
ATpoint
78k
What is the question exactly? With only 20 genes you basically **must** use the spike-ins as that few genes do not really allow to normaliz…
Comment: Building reference dbSNP file using WGS samples
by
analyst
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10
Dear [Brian][1] I realized that problem is with callvariants.sh script because when I called variants using freebayes I did not find aforem…
Comment: gatk SelectVariants is giving dupilicate allele error while extracting SNPs out
by
analyst
▴
10
Its bbmap tool callvariants.sh. I think you are right because I did not get such error when I called variants through freebayes.
Answer: Efficient way of calculating the number of mismatches between two sets of sequen
by
j.gleixner
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0
Since all your sequences have the same length (say M) and you are only looking concerned with hamming distance you can encode your sequence…
Comment: Where to download excel file to include major human disease, prevalence and inci
by
GenoMax
136k
ChatGPT says
Disease Prevalence Approximate Number of Cases (Worldwide)
Cardiovascular Diseases High Over 17 million deaths annual…
Comment: Where to download excel file to include major human disease, prevalence and inci
by
Pierre Lindenbaum
158k
using wikidata: https://query.wikidata.org/sparql?query=%0ASELECT%20%3Fitem%20%3FitemLabel%20%3FitemDescription%20%3Fprevalence%20%3Fdoid%0…
Comment: Opinion on miRNA pipeline
by
ju_ra
•
0
Thank you very much! I see you decided to go for Bowtie as aligner. Do you see any issue in using STAR (as a splice aware reader technicall…
Answer: How to avoid missannotated GO terms?
by
Elisabeth Gasteiger
★
2.3k
Please contact the UniProt helpdesk whenever you find such annotations, especially in these cases where the GO evidence/source tag says "Un…
Comment: gatk SelectVariants is giving dupilicate allele error while extracting SNPs out
by
Pierre Lindenbaum
158k
again, it's a problem with the variant caller, which is ?
Comment: gatk SelectVariants is giving dupilicate allele error while extracting SNPs out
by
analyst
▴
10
Not only opposite case but same case nucleotides are also present in vcf fle.
![enter image description here][1]
[1]: /media/images/4…
Comment: gatk SelectVariants is giving dupilicate allele error while extracting SNPs out
by
analyst
▴
10
Yes [Pierre][1] there is lower case **g** in **REF** and upper case **G** in **ALT** field. My question is that why variant caller is calli…
Answer: gatk SelectVariants is giving error while extracting SNPs out of vcf file
by
Pierre Lindenbaum
158k
This is an error in your input vcf file. The REF allele MUST be différent from the ALT allele.
Comment: gatk SelectVariants is giving error while extracting SNPs out of vcf file
by
analyst
▴
10
I observed that my reference genomic fasta file contains both lower case and upper case nucleotides.
Do I need to convert lower case nucle…
Comment: Building reference dbSNP file using WGS samples
by
analyst
▴
10
I observed that both lower and upper cases are present in reference fasta file. Is bbtool case sensitive that while calling variants it con…
Comment: Read count vs Depth
by
Mary
•
0
Thanks Brain Bushnell
Referring to my query1: So u mean that for a particular gene, if total read count is 6, then depth may be just 1 or …
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