Using tophat results via UCSC genome browser

statsteam · 09-14-2009, 02:38 PM

Hi all,

Recently, I ran TopHat with 76bp reads data and got the results (sam, bed, and wig files).

Actual a few lines of my input (fasta file) are:
>HWUSI-EAS366:4:1:4:624#0/1:
CTCNGGATGGAGTACAGTGGTGTGATCATGGCTCACTGTAGNNNNNANCNCNTGGGCGCAAGCNNNNNNNNNCTAN
>HWUSI-EAS366:4:1:4:243#0/1:
CGGNGCCGTTGCTGGTTCTCACACCTTTTAGGTCTGTTCTCNNNNNCNGNTNCGACTCTCTCTNNNNNANNNCCGN
>HWUSI-EAS366:4:1:4:1373#0/1:
GAAAAAACCACCCAGCGGTGATGGCAGCGCGCGTGGGTCCCNNNGNGNGNGGGGCGGGTCGCGCNNNNGNNNCGAN
>HWUSI-EAS366:4:1:4:1672#0/1:
GGGCAGGAAAAAAAGGGAAGANAAAATACTGGGGAAGAAAANNNANCNCNGTTTGGCAGCTCTTNNNNGNNNCAGN

And a few lines of junctions.bed file are:

track name=junctions description="TopHat junctions"
gi|29823169|ref|NT_025004.13|Hs18_25160 9690 19656 JUNC00000001 1 + 9690 19656 255,0,0 2 37,38 0,9928
gi|29823169|ref|NT_025004.13|Hs18_25160 14260 19654 JUNC00000002 2 + 14260 19654 255,0,0 2 57,36 0,5358
gi|29823169|ref|NT_025004.13|Hs18_25160 19701 160104 JUNC00000003 3 + 19701 160104 255,0,0 2 32,66 0,140337

A few lines of coverage.wig file are:

track type=bedGraph name="TopHat - read coverage"
gi|29823169|ref|NT_025004.13|Hs18_25160 0 9580 0
gi|29823169|ref|NT_025004.13|Hs18_25160 9580 9655 1
gi|29823169|ref|NT_025004.13|Hs18_25160 9655 9690 0

Here is the problem.

When I copied and pasted the results (either bed file or wig file), I always got an error and when I change the gi|29823169|ref|NT... part to something like chromosome name, it works.

As you can see from my input file, I don't have gi|29823169|ref|NT... part. I am not sure where the TopHat find such label or reference.

Can someone tell me what gi|29823169|ref|NT... part means and how I can convert these files into the one that UCSC genome brower understands. I think I need to get the actual chromosome names.

Thank you,
Statsteam

DrD2009 · 11-18-2009, 08:49 AM

You might give Galaxy a try: http://main.g2.bx.psu.edu/

On there you can upload the file and manipulate it into a format that you can use. I'm pretty new to bioinformatics so there might be a faster and easier way, but thus far it has been a very useful tool. Since you are wanting to upload the data to UCSC it would probably be best to place your data into a GFF file. I can give you a little walk through on using Galaxy to convert your BED file into a GFF.

1. Go to http://main.g2.bx.psu.edu/
2. Click 'Get Data' and then 'Upload File' select your file as a BED file and then browse for your file, select it, and then click Execute.
3. Your data should be in separate columns automatically by selecting the file type as BED which should convert the pipes into tabs. From here it is just simple text manipulation.
4. Click on 'Text Manipulation' and then you can manipulate your file by adding the necessary columns for the GFF format and then you can just simply cut them using the 'Cut' option to put them in order.

Hope this helps.

-Brandon

HTS · 11-20-2009, 12:37 PM

Alternatively, you could download hg18/19 indexes from the Bowtie website and use them from now on (what you see now is a result of using the indexes built by NCBI assemblies), which use chromosome names consistent with the UCSC genome browser (chr1, chr2 etc), if you don't want to edit/run things yourself.

Cheers,

-- Leo

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09-14-2009, 02:38 PM	#1
statsteam Member Location: Californica Join Date: Sep 2009 Posts: 19	Using tophat results via UCSC genome browser Hi all, Recently, I ran TopHat with 76bp reads data and got the results (sam, bed, and wig files). Actual a few lines of my input (fasta file) are: >HWUSI-EAS366:4:1:4:624#0/1: CTCNGGATGGAGTACAGTGGTGTGATCATGGCTCACTGTAGNNNNNANCNCNTGGGCGCAAGCNNNNNNNNNCTAN >HWUSI-EAS366:4:1:4:243#0/1: CGGNGCCGTTGCTGGTTCTCACACCTTTTAGGTCTGTTCTCNNNNNCNGNTNCGACTCTCTCTNNNNNANNNCCGN >HWUSI-EAS366:4:1:4:1373#0/1: GAAAAAACCACCCAGCGGTGATGGCAGCGCGCGTGGGTCCCNNNGNGNGNGGGGCGGGTCGCGCNNNNGNNNCGAN >HWUSI-EAS366:4:1:4:1672#0/1: GGGCAGGAAAAAAAGGGAAGANAAAATACTGGGGAAGAAAANNNANCNCNGTTTGGCAGCTCTTNNNNGNNNCAGN And a few lines of junctions.bed file are: track name=junctions description="TopHat junctions" gi\|29823169\|ref\|NT_025004.13\|Hs18_25160 9690 19656 JUNC00000001 1 + 9690 19656 255,0,0 2 37,38 0,9928 gi\|29823169\|ref\|NT_025004.13\|Hs18_25160 14260 19654 JUNC00000002 2 + 14260 19654 255,0,0 2 57,36 0,5358 gi\|29823169\|ref\|NT_025004.13\|Hs18_25160 19701 160104 JUNC00000003 3 + 19701 160104 255,0,0 2 32,66 0,140337 A few lines of coverage.wig file are: track type=bedGraph name="TopHat - read coverage" gi\|29823169\|ref\|NT_025004.13\|Hs18_25160 0 9580 0 gi\|29823169\|ref\|NT_025004.13\|Hs18_25160 9580 9655 1 gi\|29823169\|ref\|NT_025004.13\|Hs18_25160 9655 9690 0 Here is the problem. When I copied and pasted the results (either bed file or wig file), I always got an error and when I change the gi\|29823169\|ref\|NT... part to something like chromosome name, it works. As you can see from my input file, I don't have gi\|29823169\|ref\|NT... part. I am not sure where the TopHat find such label or reference. Can someone tell me what gi\|29823169\|ref\|NT... part means and how I can convert these files into the one that UCSC genome brower understands. I think I need to get the actual chromosome names. Thank you, Statsteam

11-18-2009, 08:49 AM	#2
DrD2009 Member Location: Kansas City Join Date: Oct 2009 Posts: 88	You might give Galaxy a try: http://main.g2.bx.psu.edu/ On there you can upload the file and manipulate it into a format that you can use. I'm pretty new to bioinformatics so there might be a faster and easier way, but thus far it has been a very useful tool. Since you are wanting to upload the data to UCSC it would probably be best to place your data into a GFF file. I can give you a little walk through on using Galaxy to convert your BED file into a GFF. 1. Go to http://main.g2.bx.psu.edu/ 2. Click 'Get Data' and then 'Upload File' select your file as a BED file and then browse for your file, select it, and then click Execute. 3. Your data should be in separate columns automatically by selecting the file type as BED which should convert the pipes into tabs. From here it is just simple text manipulation. 4. Click on 'Text Manipulation' and then you can manipulate your file by adding the necessary columns for the GFF format and then you can just simply cut them using the 'Cut' option to put them in order. Hope this helps. -Brandon

11-20-2009, 12:37 PM	#3
HTS Member Location: Toronto Join Date: Nov 2009 Posts: 24	Alternatively, you could download hg18/19 indexes from the Bowtie website and use them from now on (what you see now is a result of using the indexes built by NCBI assemblies), which use chromosome names consistent with the UCSC genome browser (chr1, chr2 etc), if you don't want to edit/run things yourself. Cheers, -- Leo