btw I asked him to also post this question to the new google group since it's a very good question!

• https://groups.google.com/forum/#!forum/integrated-genome-browser-help-desk

• I was able to add a local server and load BED file types of the tomato genome with IGB.
• I attempted to load BAM files. The row for the data changed from grey to white, indicating that the file had been loaded, but no data appeared on-screen.
• Dr. Freese suggested that I may be looking at a point where no data was present to be displayed and gave the location: SL4.0ch01:32,433,077-32,602,167 where data is known to be present.
• I went to those coordinates in IGB for the tomato genome and loaded the comparable BAM file (H1-C.bam) from IGB's RNA-Seq quickload; I was able to see the data at that location.
• I attempted to open a local copy of that first H1-C.bam file from my server I had added to IGB quickload. The computer locked up and I had to hard restart.
• From then on opening IGB results in a complete lock up, sometimes even when the program is only opened and given no tasks, sometimes a few tasks can be completed.
• I tried clearing the cache per the transvar guide: https://wiki.transvar.org/pages/viewpage.action?pageId=19005897
• I uninstalled IGB and removed all IGB associated files from the computer.
• I redownloaded IGB from Bioviz.org and reinstalled, but the computer will still lock up shortly after launch of IGB.

For reference, the locations of the files I used in this testing:
S_lycopersicum_Sep_2019 Solanum lycopersicum (Sep 2019) tomato (SL4.0)
BAM files: http://lorainelab-quickload.scidas.org/rnaseq/S_lycopersicum_Sep_2019/PGRP1939255/
BED files:
http://www.igbquickload.org/quickload/S_lycopersicum_Sep_2019/

Quick followup:

• Please attached the annots.xml file you created, if any.

cc: Logan Weidenhammer

The original had been deleted. I believe the the annots.xml file only contained the following while testing the BAM file.

<files>
<file
name="PGRP1939255/H1-C.bam"
title="Pollen Tube PGRP1939255/Reads/H.C.1 - Heinz control replicate 1 alignments"
description="read alignments"
url="S_lycopersicum_Sep_2019/PGRP1939255"
background="ffffff"
foreground="00C5CD"
max_depth="10"
show2tracks="false"
direction_type="arrow"
/>
</files>

And this while testing the BED file:

<files>
<file
name="S_lycopersicum_Sep_2019.bed.gz"
title="ITAG4.0"
description="ITAG4.0 gene models, 4.0 genome assembly"
url="S_lycopersicum_Sep_2019"
foreground="000000"
name_size="14"
direction_type="arrow"
label_field="id"
background="FFFFFF"
load_hint="Whole Sequence"
show2tracks="true"
/>
</files>

The current instructions on the “Create a satellite IGB QuickLoad site” page are up to date and accurate to the current version of IGB.

Dr. Freese and I identified the reason the BAM file was not working originally. It looks like the http://www.igbquickload.org/quickload/ site where I was getting my test files does not allow internet browsers to download these large BAM files. We tested a smaller BAM file for the tomato genome and it worked normally.

Observations:

I had trouble at first finding the location of the Data Sources window. I think it would be useful to add a link to the page https://wiki.transvar.org/display/igbman/Data+Sources+Tab or a copy of the “Introduction” section on that page to the page https://wiki.transvar.org/display/igbman/Adding+and+Managing+Data+Source+Servers.

I also had trouble with refreshing my data source server on IGB after making changes to the files on my local machine. Selecting the ‘refresh server’ icon on the left does not load any new files added to the source. The user must remove the server from “Data Sources” and add it again. This instruction could also be added to the page: https://wiki.transvar.org/display/igbman/Adding+and+Managing+Data+Source+Servers

I will make a ticket about implementing these changes.

IGBF-2454 created.

Thanks for the detailed notes Logan Weidenhammer and Nowlan Freese !

[~aloraine] Do we want to investigate the http://www.igbquickload.org/quickload/ large-file download problem?

The issue I ran into was on the scidas server: http://lorainelab-quickload.scidas.org/rnaseq/S_lycopersicum_Sep_2019/PGRP1939255/

The scidas data load in IGB and I can curl the data on my laptop, but clicking on the file and trying to download through the browser appears to be blocked.

I am OK with this as it could protect people from accidentally try to download a multi-Gb sized file.

Moving to closed.