Hello, I am attempting to generate a FASTA from MACS2 generated summits bed file using Galaxy's workflow: "Create MEME-ChIP input FASTA file (500bp centered regions) from MACS2 summits.bed file". This MACS2 bed file was generated from bowtie2 alignment bam file. Homo_sapiens.GRCh38.dna.primary_assembly (downloaded from ensembl) was used as a reference genome. However, when seemingly the same assembly (hg38) was used to fetch sequences I have a following message: 18783 warnings, 1st is: Unable to fetch the sequence from '181351' to '500' for chrom '1'. Skipped 18783 invalid lines, 1st is #1, "1 181351 181851 ag_m_peak_1 30.56049", and nothing was extracted to FASTA. Could you please suggest me any solution? Thanks Konstantin
There is either a 1) problem with the formatting of the Custom genome or there is a 2) chromosome naming mismatch problem between the inputs. Any
bed input also needs to be formatted correctly for the datatype specification/chromosome naming.
These topics are covered in the Support FAQs here, including how to submit a bug report for more direct help: https://galaxyproject.org/support/#troubleshooting
Thanks! Jen, Galaxy team