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Shicheng Guo
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Recent Replies
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
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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…
Comment: Building reference dbSNP file using WGS samples
by
analyst
▴
10
Dear [Brian][1] do I need to convert lower case nucleotides into upper (all nucleotides in one case) and perform variant calling again?
…
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: Building reference dbSNP file using WGS samples
by
analyst
▴
10
I performed variant calling again using callvariants.sh script.
Now I am getting this error while extracting snps out of merged vcf file:
…
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 …
Comment: how to draw the valcano plot for DEGs in a different way
by
CTLong
▴
30
From you Limma DEG results, you could use `glimmaMA` to generate a MA plot as demonstrated in this vignette (https://bioconductor.org/packa…
Comment: How to avoid missannotated GO terms?
by
Dr.Animo
▴
80
These kind of missannotations are assigned to multiple plant proteins except few like Arabidopsis thaliana and Zea maize. The problem is if…
Answer: SQL request from NCBI metadata and stat_analysis tables
by
zorbax
▴
600
I think what you are looking for is the LEFT JOIN approach, where you can select a specific phylum. Have you tried this (next you should or…
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