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Comment: create 'negative' bed annotation from bed

Comment: How to find the read counts of sequences present in a file?

Comment: How To Convert Gencode Gtf Into Bed Format ?

Answer: How To Convert Gencode Gtf Into Bed Format ?

Comment: add 1/2 to fastq header

EdgeR installation in Mac 1 Pro (M1 chip) using Studio

Answer: Why do annotating the same functionality with different databases produce differ

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Popular Question to steve ★ 3.3k

Recent Replies

Comment: create 'negative' bed annotation from bed by joe ▴ 300

Exactly what I need, thanks!

Comment: fcoex co-expression analysis by andres.firrincieli 3.0k

If Myc is not included in any module what does that mean?

Comment: create 'negative' bed annotation from bed by ATpoint 66k

bedtools complement

Comment: How to find the read counts of sequences present in a file? by khq5801 ▴ 10

![enter image description here][1] [1]: /media/images/185dc782-c875-49f4-996d-def808a4

Comment: Problems with perl-xml-parser-2.44-4 by Юлия ▴ 10

Please could you explain hoe to make Makefile.PL in my case?

Comment: How To Convert Gencode Gtf Into Bed Format ? by leshaker • 0

needed to google it myself but like the approach! https://github.com/dputhier/pygtftk

Comment: Different results in finding human sequences from metagenomes (bowtie2 and Krake by GenoMax 123k

You can try `removehuman.sh` which is part of BBMap suite: https://www.seqanswers.com/forum/bioinformatics/bioinformatics-aa/37175-introduc…

Comment: Why can't I quantify the peaks (scATAC)? by LChart 1.5k

You define the object `frag.104` with a 4; but you reference object `frag.101` with a 1; is this intended?

Comment: What is the default/best practice to map prob IDs to gene IDs by Nemo • 0

Thanks @barslmn, I know how to find matched gene with each prob. But the problem is in the input expression matrix after mapping to genes, …

Comment: Different results in finding human sequences from metagenomes (bowtie2 and Krake by Medhat 9.4k

I moved this to a comment as it is not an answer.

Comment: Problems with perl-xml-parser-2.44-4 by Mensur Dlakic ★ 21k

Much better, thank you. It seems pretty clear that this package requires a very narrow range of perl versions - `>=5.22.0 and <5.23.0` can'…

Comment: Different results in finding human sequences from metagenomes (bowtie2 and Krake by kmat • 0

Thank you for your reply :-) I wondered if the bowtie2 results were too strict or if the Kraken2 results were too permissive... If anyone …

Comment: how to calculate BAF and LRR from bam or vcf file by BioKeystone • 0

BAF b allele frequency LRR log R ratio

Comment: Left Join Issue in R by cthangav ▴ 40

I believe removing the duplicates from add using the following command fixed the issue. Thank you add2 <- add %>% dplyr::distinct(ADDG…

Answer: Why does `bowtie` only find perfect matches even when specifying mismatches? (ie by swbarnes2 13k

You can't tell the number of mismatches from the CIGAR. Just insertions, deletions, clippings, etc.

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