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Old 07-17-2011, 05:19 AM   #1
Sheera
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Default Visulisation of gene arrangements on Chromosomes!

Hello!
I was looking for some software to visualise the gene arrangement on chromosome in humans.

I have both gene coordinates and the fasta sequences.
IGV looked to serve my purpose but it need the file in BAM/SAM format.
I was trying to change my files into BAM format using bowtie but it gives me error!
Please truncate reads and quality values and and re-run Bowtie

I think it is because i have whole gene sequences.
Can you suggest me some other tool or way to overcome this error!

I googled a lot but in vain!
Thanks in advance!
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Old 07-17-2011, 09:52 AM   #2
biznatch
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Do you want to see all the genes on a chromosome or just specific ones?

UCSC Genome Browser, you can visualize all the genes in the human genome by viewing one chromosome at a time. If you have specific genes/data you want to visualize, you can create your own custom track of just the genes you're interested in. A .bed file is probably the easiest.
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Old 07-17-2011, 01:02 PM   #3
Sheera
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I just want some specific genes (of my interest), can I create .bed file with just gene coordinates?
Where can this .bed file be visualised?
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Old 07-17-2011, 08:08 PM   #4
biznatch
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Yes you can create a bed file with your genes of interest. For your data, it would probably include 4 columnes, tab seperated. First column is chromosome (eg. chr3, chrX), second is gene transcription start site, third is stop site, fourth is gene name. See the link in my previous post for more information on .bed files. To add the track in the UCSC browser click "Add Custom Track". This would basically show a black bar for each gene, along with the gene name.
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Old 07-17-2011, 11:20 PM   #5
Jim Robinson
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You can also load the .bed file in IGV, it does not require SAM/BAM format, and in fact .BED format is more appropriate for what you want to view. SAM/BAM is recommended (but again not required) for viewing alignments.

Best

Jim
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Old 07-18-2011, 03:52 AM   #6
Sheera
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Thanks everyone!
I tried both : Genome Browser and IGV.

IGV worked fine but I couldnt get any desired views.
It doest show the orientations and all the genes were clustered!
n with Genome Browser, i get this error

File 'coordinate.bed' - Error line 5 of custom track: chromStart after chromEnd (27778313 > 27777841)

The .bed file that I was using is as follows

browser position chr6:25800000-27900000

browser pack all

track name=coords description="Chromosome coordinates list" visibility=2
chr6 26031816 26032287 HIST1H3B

chr6 27778313 27777841 HIST1H3H

chr6 26241020 26240653 HIST1H4F

chr6 26104564 26104160 HIST1H4C

chr6 27839622 27840098 HIST1H3I

chr6 26107639 26108363 HIST1H1T

chr6 26197011 26199463 HIST1H3D

chr6 26216427 26216871 HIST1H2BG

chr6 26273639 26273203 HIST1H2BI


I couldn't figure out how to resolve this error!
ANy suggestion ?
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Old 07-18-2011, 04:18 AM   #7
Eric Fournier
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Quote:
Originally Posted by Sheera View Post
Thanks everyone!
File 'coordinate.bed' - Error line 5 of custom track: chromStart after chromEnd (27778313 > 27777841)
The error essage plainly states that your start coordinate is larger than your end coordinates. Reverse them.

In the UCSC genome browser, coordinates are always specified in increasing order, regardless of the strand, which is usually specified in an extra column.
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Old 07-18-2011, 04:48 AM   #8
Sheera
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I tried that already and again but I get this error know

Unrecognized format line 4 of custom track: 6 26158348 26171576 HIST1H2BD 1 (note: chrom names are case sensitive)


My new file looks like:
browser position chr6:25800000-27900000

browser pack all

track name=coords description="Chromosome coordinates list" visibility=2

6 26158348 26171576 HIST1H2BD 1

6 26158348 26171576 HIST1H2BD 1

6 27100816 27103070 HIST1H2AG 1

6 26156558 26157342 HIST1H1E 1

6 26217147 26217710 HIST1H2AE 1

6 26124372 26124917 HIST1H2AC 1


Does .bed file needs gene name in small letter or the orientation could only be in +/- format?
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Old 07-18-2011, 04:54 AM   #9
Eric Fournier
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Quote:
Originally Posted by Sheera View Post

Unrecognized format line 4 of custom track: 6 26158348 26171576 HIST1H2BD 1 (note: chrom names are case sensitive)
Read the error message attentively. "chrom names are case sensitive" should give you a hint. You changed your chromosome names from "chr6" to "6". In the UCSC genome browser, chromosome names take the form "chrX".
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Old 07-18-2011, 05:06 AM   #10
Jim Robinson
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To answer your other questions, yes you need to use "+" and "-" to specify strand. Also, to "uncluster" the genes in IGV right-click and select "Expanded". By default IGV collapses features to a single row. UCSC calls this "dense" mode if I'm not mistaken.
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Old 07-19-2011, 09:07 AM   #11
Sheera
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Thanks a lot everyone, it really helped to get acquainted with both Genome Browser and IGV.
But there is no end to the questions.

I want to know is there any tools/ module that can help me to randomise my gene coordinates and calculate some value to get their arrangement on the chromosomes?
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Old 07-22-2011, 10:12 PM   #12
mjp
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Have you tried circos ?
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