I have a problem when trying to get genomic DNA sequences from a list of genomic coordinates. The file contains regions aroung ChIP-seq peaks and has been obtained trough several Galaxy functions (Map with Bowtie, MACS2 callpeak, compute and cut). It is correctly formatted (as .interval, but I have also tried as .bed) with columns corresponding to chr start end name and its genome version is indicated: [format:interval database:mm9].
When I apply the function “Extract Genomic DNA using coordinates from assembled/unassembled genomes” selecting mm9 from the locally cached genomes I get an empty file with this warning:
*622 warnings, 1st is: Chromosome by name ‘chr19’ was not found for build ‘mm9’. *
Skipped 622 invalid lines, 1st is #1, “chr19 3204403 3204904 SAM-to-BAM_on_data_7__converted_BAM_peak_1”.
I get the same when I try to redo the analysis selecting mm10 instead of mm9.
Note that in https://usegalaxy.org/ there are two instances of “Extract Genomic DNA using coordinates from assembled/unassembled genomes”, one is version 3.0.3 (the same available in https://usegalaxy.eu/) but there is also a version 2.2.4 which works perfectly fine on the same .interval file above and it returns the correct fasta file with all the sequences.
Moreover, in https://usegalaxy.org/ the version 3.0.3 of “Extract Genomic DNA using coordinates from assembled/unassembled genomes” does not even display mm9 among the available cached genomes (even If I do the entire pipeline including mapping).
I need to perform this step on https://usegalaxy.eu/, can you help me with this?