Community Digest

Top new questions this week:

Convert FASTA to FASTQ with dummy quality scores

I have a FASTA file which I would like to convert into FASTQ format as the tool I want to use my data in requires it in FASTQ format. So dummy quality scores are fine. Note: I am not using any ...

fasta fastq  
asked by Michael Hall 4 votes
answered by Michael Hall 2 votes

renaming IDs in gff3 with BCBio.GFF

I wrote a script which should changes IDs in a GFF3 file. Unfortunately, the below script has two problems. It attaches the new ID to Parent which leads that Parent contains the old and new id. How ...

annotation biopython gff3  
asked by user977828 1 vote

Greatest hits from previous weeks:

How to obtain .bed file with coordinates of all genes

I want to get a .bed file with the genes' names and canonical coordinates, also I would like to have coordinates of exons, too. I can get the list from UCSC, however, if I choose UCSC Genes - ...

bed public-databases  
asked by German Demidov 11 votes
answered by Alex Reynolds 13 votes

How to count reads in bam per bed interval with bedtools

I recently installed Ubuntu 16.04 (because I was still using 12.04). But it seems my bedtools scripts don't work properly anymore. I can't figure out how to use the new bedtools for my old ways. What ...

bam bedtools  
asked by benn 7 votes
answered by Devon Ryan 5 votes

What is the difference between FASTA, FASTQ, and SAM file formats?

I'd like to learn the differences between 3 common formats such as FASTA, FASTQ and SAM. How they are different? Are there any benefits of using one over another? Based on Wikipedia pages, I can't ...

file-formats fasta fastq sam  
asked by kenorb 20 votes
answered by Konrad Rudolph 34 votes

BLAST(n): No hits found

I am currently exploring the BLAST program, just for testing purpose i generated two FASTA files, containing two genes A and B, such that B is just a motif of repeated 'G's that occurs in A. file ...

sequence-alignment blast  
asked by Paul 6 votes
answered by terdon 8 votes

Script to allow gene set enrichment analysis of 10x genomics data in R

I have 10x single cell RNA seq data. Which R package is best suited for analysis of the 10x data matrix. What is the script to prepare the data for downstream GSEA analysis. I have already processed ...

r scrnaseq 10x-genomics gsea cellranger  
asked by Jay 5 votes
answered by Ian Sudbery 5 votes

Remove/delete sequences by ID from multifasta

I have a fasta file like this: >Id1 ATCCTT >Id2 ATTTTCCC >Id3 TTTCCCCAAAA >Id4 CCCTTTAAA I want to delete sequences that have the following IDs. Id2 Id3 The IDs are in a .txt file, ...

fasta shell  
asked by andresito 3 votes
answered by Kamil S Jaron 6 votes

How can I calculate gene_length for RPKM calculation from counts data?

I have read counts data and I want to convert them into RPKM values. For this conversion I need the gene length. Does the gene length need to be calculated based on the sum of coding exonic lengths? ...

gene gtf gencode fpkm  
asked by user3351523 10 votes
answered by Devon Ryan 4 votes
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