| 2017-11-10 06:34:47 -0600 | commented answer | Stranded Paired-end RNA-seq coloring and wig/bw support Thanks for the answer - didn't know about wig support, that is at least something, even if the files are huge and the conversion process takes time. Hopefully other features can be added in at a later time, the interface of GenomeBrowse is so much superior to other options! |
| 2017-11-10 06:34:29 -0600 | answered a question | Stranded Paired-end RNA-seq coloring and wig/bw support Thanks for the answer - didn't know about wig support, that is at least something, even if the files are huge and the conversion process takes time. Hopefully other features can be added in at a later time, the interface of GenomeBrowse is so much superior to other options! |
| 2017-11-03 05:06:12 -0600 | received badge | ● Enthusiast |
| 2017-10-24 08:19:14 -0600 | asked a question | Stranded Paired-end RNA-seq coloring and wig/bw support Hello, GenomeBrowse is by far my favorite genome browser, but it has a two shortcomings that prevent me from using it from everything (and recommending it to everyone I know). One issue is the visualization of stranded, paired end RNA-seq - in IGV you have the option to color by 'first in strand', so that the mate pairs both have the same color, which allow you to visualize strand specificity for reads. Right now in GenomeBrowse it colors both mates separately, and with Illumina since they both are on different strands, you get a mix of forward and reverse-colored reads no matter the actual strandness of the pair. Second issue is no wig or bigwig support, which prevents the import of most publicly available tracks (say from UCSC) without downloading the FASTQ and remapping to BAM. GenomeBrowse lacking this feature is somewhat puzzling, as these file formats are straightforward (at least compared to BAM) and very similar to coverage plots that it produces itself from BAM files. Now I understand that both these use cases are not directly linked to other products in the suite of Golden Helix, but they would make GenomeBrowse usable for all common analysis scenarios. Please consider the implementation of both these features. |
| 2014-08-15 03:54:13 -0600 | received badge | ● Notable Question |
| 2014-08-14 11:55:04 -0600 | answered a question | custom reference : Unable to find reference sequence source for build Thanks for the amazing level of support as always. I got it to work with your instructions but it has weird behavior. It will only work with the .tsf from the GenomeBrowse distribution, not with the .tsf I generated from the GRCh37g1k.fasta file from ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/humang1kv37.fasta.gz - I'll try to investigate the difference. Also, I had to copy the file to /Data, because it was in /CommonData which is not searched by gautil by default. Also, from a technical point of view, its weird that the path parameter in --refFolder must be enclosed within "", while the source is not - I expected to do --refFolder G:\ Any way, it works now, so now I can precalculate coverages :) Thank you so much, Michael |
| 2014-08-14 07:19:52 -0600 | answered a question | custom reference : Unable to find reference sequence source for build Encountering the same problem, even with giving the .tsf file as a -ref parameter. Doesn't work in Unix and Windows, latest builds. I built the .tsf file from the fasta I mapped to, GRCh37g1k. The documentation of the gautil functions could use some work, there's a lot of ambiguity for the parameters it expects, as well as many typos. |