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Answer: I have performed Trimmomatic run for adapter removal. QC report shows drop in th

Comment: Assistance with Fungal Genome Annotation Using Maker and BLAST

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Scholar to Pierre Lindenbaum 157k

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Recent Replies

Comment: How to find out what adapters to remove after FastQC of RNAseq data? by ella • 0

Thank you for the fast help, I have the BBMap suite installed anyways and will try it out :)

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: SCENIC-openloom not working by kyriakds • 0

Hello, Did you find a solution in the end?

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 • 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.

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