Question: Wig/BedGraph-to-bigWig fails with "hashMustFindVal: '1' not found Error running wigToBigWig."
0
gravatar for skeffington
3.6 years ago by
European Union
skeffington0 wrote:

Hi,

I have a very large, merged BAM file which I successfully converted to a bedgraph using the "Create a BedGraph of genome coverage" tool. I was then trying to convert this file to bigwig format (to aid viewing with IGV) using the Wig/BedGraph-to-bigWig tool with the default settings. However, I get the following error:

hashMustFindVal: '1' not found Error running wigToBigWig. Error running wigToBigWig.

I used the same (custom) genome assembly for the whole process, and the correct genome is applied in the attributes section of the input file. 

Any help or ideas would be much appreciated!

Alastair

ADD COMMENTlink modified 3.6 years ago • written 3.6 years ago by skeffington0
1
gravatar for Hotz, Hans-Rudolf
3.6 years ago by
Switzerland
Hotz, Hans-Rudolf1.8k wrote:

Hi Alastair

Despite using the "same genome for the whole process", it suspiciously sounds like a "chr1 versus 1" problem. Have a look at: http://redmine.soe.ucsc.edu/forum/index.php?t=msg&goto=10745&S=2a335135e76cf9b7160c0e9d41353767

 

Hans-Rudolf

 

ADD COMMENTlink written 3.6 years ago by Hotz, Hans-Rudolf1.8k

Hi Hans-Rudolf,

Thanks for your comment. I admit it does look like that sort of problem, but I have only one genome file, which I have used for every step of the procedure, so there shouldn't be any chromosome name mismatches. The genome file has several hundred contigs that derive from two sources: first, the original JGI genome assembly and second, subsequent assemblies of reads not included in the JGI assembly. Hence the name format of the contigs is not consistent: some names are just digits, others have the form "contig_digits" and others "scaffold_digits". I wonder if this could be causing problem? I provide a link to a "genome.txt" file which lists the "chromosomes" and their sizes, so you can see what I mean:

http://de.iplantcollaborative.org/dl/d/18185958-79EA-48FF-9440-4A12908D4F2F/genome.txt

Thanks!

Alastair

 

ADD REPLYlink written 3.6 years ago by skeffington0

Hi Alastair

I don't think the contig names in the genome,txt file are cusing troubles. I am actually more concerned about the total number of "chromosomes" you have:  12744      How do you wanna a look at those in IGV (or Galaxy trackster)?

Maybe it will help filter the bam file to those contigs you are actually intersted in?

Hans-Rudolf

 

ADD REPLYlink written 3.6 years ago by Hotz, Hans-Rudolf1.8k

Hi Hans-Rudolf,

So you think the large number of "chromosomes" is causing trouble for the bedgraph-to-bigwig tool? I don't think it's critical that it's in bigWig format, so maybe I'll give up.

This is the world of non-model organisms with rather imperfect genome assemblies.I'm really an experimentallist, trying to create a resource for myself and others in my group. We do lots of proteomic experiments which identify proteins and genes that are potentially involved in our process of interest. When we identify such a GOI we need to be able to assess the evidence for the gene models at that locus such that we can plan subsequent experiments. Thus I'm mapping the available gene models from the JGI predictions to our improved genome, as well as all available RNAseq data. For the latter I was summarizing the results in a single bedgraph. I can view this perfectly well for a locus of interest in the IGB, and I've made a quickload site for everyone in our group to access, but I wanted to explore what IGV has to offer as well. 

Cheers,

Alastair

ADD REPLYlink written 3.6 years ago by skeffington0

Have you tried generating the bigWig file on the command line?

ADD REPLYlink written 3.6 years ago by Hotz, Hans-Rudolf1.8k

not yet, but I should give it a go - I'm much more comfortable in linux than I was two weeks ago - much thanks to all the professional bioinfomaticians on sites like this that give their time to answer my questions!

ADD REPLYlink written 3.6 years ago by skeffington0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 124 users visited in the last hour