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Pierre Lindenbaum
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Recent Replies
Comment: How to make alpha diversity boxplot?
by
yeah
•
0
thanks a lot! can't believe that is so simple
Comment: how to identify uniq genes between two gff files.
by
nikhil
▴
10
yes got it, thank you very much.
Comment: I have performed Trimmomatic run for adapter removal. QC report shows drop in th
by
Vijith
▴
30
@swbarnes2, thanks for the response, by the way, can you tell me why/ how this happens during the sequencing process, and if it could negat…
Comment: how to identify uniq genes between two gff files.
by
Pierre Lindenbaum
157k
> can you explain this ??
yes. you should use options like `-u` .
> Write original A entry once if any overlaps found in B. In other word…
Comment: how to extract unique snps in a vcf file by comparing with multiple vcf files
by
Pierre Lindenbaum
157k
so validate the answer to close the question please (Green tick on the left).
Comment: how to identify uniq genes between two gff files.
by
nikhil
▴
10
hi Pierre Linderbaum,
after extracting genes, I have 5846 genes in afile.bed and 4456 genes in bfile.bed , while
using bedtools intersec…
Comment: how to extract unique snps in a vcf file by comparing with multiple vcf files
by
nikhil
▴
10
thank you, bcftools isec is working well.
Comment: how to identify uniq genes between two gff files.
by
Pierre Lindenbaum
157k
please, comment or validate the answers to your previous questions: https://www.biostars.org/p/9573151/#9573158 ; https://www.biostars.org/…
Answer: how to identify uniq genes between two gff files.
by
Pierre Lindenbaum
157k
extract genes (e.g: awk '($3=="gene") {printf("%s\t%d\t%s\n",$1;int($4)-1,$5);}' ) from both files n sort, and use bedtools intersect with…
Answer: I have performed Trimmomatic run for adapter removal. QC report shows drop in th
by
swbarnes2
13k
G is the letter you get if there is no fluorescence.
75% of your reads have a lot of G.
I don't think this run worked.
Comment: Assistance with Fungal Genome Annotation Using Maker and BLAST
by
Edoardo
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0
I have 13,576 proteins in my file.
I tried on a small set of 3 proteins and it worked fine!
Comment: Assistance with Fungal Genome Annotation Using Maker and BLAST
by
Mensur Dlakic
★
24k
It should be faster, though you are not telling us how many proteins are in your query file.
I suggest you use as many threads as availabl…
Comment: Hisat2 index and alignment question
by
Athena
•
0
That worked! Thank you. Didn't know that was an option... now I know.
Comment: Assistance with Fungal Genome Annotation Using Maker and BLAST
by
Edoardo
•
0
I ran blastp with the following command:
blastp \
-db /path/to/Annotation_db/uniprot_fungi.fasta \
-query MYGEN.maker.output/…
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