Re: [galaxy-dev] NGS peak calling: MACS
Hi Kanwei, I am sorry, I am using a BED formatted wiggle file. Here is first few lines from my file track type=wiggle_0 name=polyA_left chrIII 329 405 1 chrIII 1841 1868 1 chrIII 1868 1917 3 chrIII 1917 1944 2 chrIII 8486 8496 1 chrIII 8496 8498 12 chrIII 8498 8504 13 chrIII 8504 8509 14 chrIII 8509 8512 15 chrIII 8512 8551 18 chrIII 8551 8562 20 chrIII 8562 8572 19 chrIII 8572 8574 8 chrIII 8574 8579 7 chrIII 8579 8580 8 chrIII 8580 8585 7 chrIII 8585 8588 6 chrIII 8588 8627 3 chrIII 8627 8655 1 each line with four required fields, they are 1| chromosome/contig ID of the reference sequence, 2| feature start position 3| feature end position and 4| feature coverage score. thnaks, Vipin T S On 27 April 2010 19:17, Kanwei Li <kanwei@gmail.com> wrote:
Hi Vipin,
What is a bed wiggle file? We support both, but not at the same time :P
Kanwei
Looks like bedgraph.. did you make sure that the datatype was set to bedgraph? How large is the data? K On Tue, Apr 27, 2010 at 1:23 PM, Vipin TS <vipin.ts@gmail.com> wrote:
Hi Kanwei,
I am sorry, I am using a BED formatted wiggle file. Here is first few lines from my file
track type=wiggle_0 name=polyA_left chrIII 329 405 1 chrIII 1841 1868 1 chrIII 1868 1917 3 chrIII 1917 1944 2 chrIII 8486 8496 1 chrIII 8496 8498 12 chrIII 8498 8504 13 chrIII 8504 8509 14 chrIII 8509 8512 15 chrIII 8512 8551 18 chrIII 8551 8562 20 chrIII 8562 8572 19 chrIII 8572 8574 8 chrIII 8574 8579 7 chrIII 8579 8580 8 chrIII 8580 8585 7 chrIII 8585 8588 6 chrIII 8588 8627 3 chrIII 8627 8655 1
each line with four required fields, they are 1| chromosome/contig ID of the reference sequence, 2| feature start position 3| feature end position and 4| feature coverage score.
thnaks, Vipin T S
On 27 April 2010 19:17, Kanwei Li <kanwei@gmail.com> wrote:
Hi Vipin,
What is a bed wiggle file? We support both, but not at the same time :P
Kanwei
Hi Kanwei, When uploading data set to the galaxy I selected the format as bed. The file size is 16 MB. regards, Vipin T S On 27 April 2010 19:25, Kanwei Li <kanwei@gmail.com> wrote:
Looks like bedgraph.. did you make sure that the datatype was set to bedgraph? How large is the data?
K
On Tue, Apr 27, 2010 at 1:23 PM, Vipin TS <vipin.ts@gmail.com> wrote:
Hi Kanwei,
I am sorry, I am using a BED formatted wiggle file. Here is first few lines from my file
track type=wiggle_0 name=polyA_left chrIII 329 405 1 chrIII 1841 1868 1 chrIII 1868 1917 3 chrIII 1917 1944 2 chrIII 8486 8496 1 chrIII 8496 8498 12 chrIII 8498 8504 13 chrIII 8504 8509 14 chrIII 8509 8512 15 chrIII 8512 8551 18 chrIII 8551 8562 20 chrIII 8562 8572 19 chrIII 8572 8574 8 chrIII 8574 8579 7 chrIII 8579 8580 8 chrIII 8580 8585 7 chrIII 8585 8588 6 chrIII 8588 8627 3 chrIII 8627 8655 1
each line with four required fields, they are 1| chromosome/contig ID of the reference sequence, 2| feature start position 3| feature end position and 4| feature coverage score.
thnaks, Vipin T S
On 27 April 2010 19:17, Kanwei Li <kanwei@gmail.com> wrote:
Hi Vipin,
What is a bed wiggle file? We support both, but not at the same time :P
Kanwei
Hi Vipin, Your file is actually not a bed file, it's a bedgraph. Please set the type to bedgraph and try it again.. On Tue, Apr 27, 2010 at 7:02 PM, Vipin TS <vipin.ts@gmail.com> wrote:
Hi Kanwei,
When uploading data set to the galaxy I selected the format as bed. The file size is 16 MB.
regards, Vipin T S
On 27 April 2010 19:25, Kanwei Li <kanwei@gmail.com> wrote:
Looks like bedgraph.. did you make sure that the datatype was set to bedgraph? How large is the data?
K
On Tue, Apr 27, 2010 at 1:23 PM, Vipin TS <vipin.ts@gmail.com> wrote:
Hi Kanwei,
I am sorry, I am using a BED formatted wiggle file. Here is first few lines from my file
track type=wiggle_0 name=polyA_left chrIII 329 405 1 chrIII 1841 1868 1 chrIII 1868 1917 3 chrIII 1917 1944 2 chrIII 8486 8496 1 chrIII 8496 8498 12 chrIII 8498 8504 13 chrIII 8504 8509 14 chrIII 8509 8512 15 chrIII 8512 8551 18 chrIII 8551 8562 20 chrIII 8562 8572 19 chrIII 8572 8574 8 chrIII 8574 8579 7 chrIII 8579 8580 8 chrIII 8580 8585 7 chrIII 8585 8588 6 chrIII 8588 8627 3 chrIII 8627 8655 1
each line with four required fields, they are 1| chromosome/contig ID of the reference sequence, 2| feature start position 3| feature end position and 4| feature coverage score.
thnaks, Vipin T S
On 27 April 2010 19:17, Kanwei Li <kanwei@gmail.com> wrote:
Hi Vipin,
What is a bed wiggle file? We support both, but not at the same time :P
Kanwei
Hi Kanwei, Let me update the data types and try to upload the bedGraph format file. Thanks for your information. I will let you know when I encounter any error in display. thanks, Vipin On 28 April 2010 01:04, Kanwei Li <kanwei@gmail.com> wrote:
Hi Vipin,
Your file is actually not a bed file, it's a bedgraph. Please set the type to bedgraph and try it again..
On Tue, Apr 27, 2010 at 7:02 PM, Vipin TS <vipin.ts@gmail.com> wrote:
Hi Kanwei,
When uploading data set to the galaxy I selected the format as bed. The file size is 16 MB.
regards, Vipin T S
On 27 April 2010 19:25, Kanwei Li <kanwei@gmail.com> wrote:
Looks like bedgraph.. did you make sure that the datatype was set to bedgraph? How large is the data?
K
On Tue, Apr 27, 2010 at 1:23 PM, Vipin TS <vipin.ts@gmail.com> wrote:
Hi Kanwei,
I am sorry, I am using a BED formatted wiggle file. Here is first few lines from my file
track type=wiggle_0 name=polyA_left chrIII 329 405 1 chrIII 1841 1868 1 chrIII 1868 1917 3 chrIII 1917 1944 2 chrIII 8486 8496 1 chrIII 8496 8498 12 chrIII 8498 8504 13 chrIII 8504 8509 14 chrIII 8509 8512 15 chrIII 8512 8551 18 chrIII 8551 8562 20 chrIII 8562 8572 19 chrIII 8572 8574 8 chrIII 8574 8579 7 chrIII 8579 8580 8 chrIII 8580 8585 7 chrIII 8585 8588 6 chrIII 8588 8627 3 chrIII 8627 8655 1
each line with four required fields, they are 1| chromosome/contig ID of the reference sequence, 2| feature start position 3| feature end position and 4| feature coverage score.
thnaks, Vipin T S
On 27 April 2010 19:17, Kanwei Li <kanwei@gmail.com> wrote:
Hi Vipin,
What is a bed wiggle file? We support both, but not at the same time :P
Kanwei
Hi Kanwei, As per the documentation on data visualization in galaxy, I had updated my data file into wiggle variableStep format. Then I tried to create a new track browser in my local galaxy instance. Unfortunately it just shows the message "Loading data ...". Few lines from my wiggle file track type=wiggle_0 name="test run" variableStep chrom=III 1841 1 1842 1 1843 1 1844 1 1845 1 1846 1 1847 1 1848 1 1849 1 1850 1 1851 1 1852 1 1853 1 Any ideas are sincerely appreciated. many thanks, Vipin T S Hi Kanwei,
Let me update the data types and try to upload the bedGraph format file. Thanks for your information. I will let you know when I encounter any error in display.
thanks, Vipin
On 28 April 2010 01:04, Kanwei Li <kanwei@gmail.com> wrote:
Hi Vipin,
Your file is actually not a bed file, it's a bedgraph. Please set the type to bedgraph and try it again..
On Tue, Apr 27, 2010 at 7:02 PM, Vipin TS <vipin.ts@gmail.com> wrote:
Hi Kanwei,
When uploading data set to the galaxy I selected the format as bed. The file size is 16 MB.
regards, Vipin T S
On 27 April 2010 19:25, Kanwei Li <kanwei@gmail.com> wrote:
Looks like bedgraph.. did you make sure that the datatype was set to bedgraph? How large is the data?
K
On Tue, Apr 27, 2010 at 1:23 PM, Vipin TS <vipin.ts@gmail.com> wrote:
Hi Kanwei,
I am sorry, I am using a BED formatted wiggle file. Here is first few lines from my file
track type=wiggle_0 name=polyA_left chrIII 329 405 1 chrIII 1841 1868 1 chrIII 1868 1917 3 chrIII 1917 1944 2 chrIII 8486 8496 1 chrIII 8496 8498 12 chrIII 8498 8504 13 chrIII 8504 8509 14 chrIII 8509 8512 15 chrIII 8512 8551 18 chrIII 8551 8562 20 chrIII 8562 8572 19 chrIII 8572 8574 8 chrIII 8574 8579 7 chrIII 8579 8580 8 chrIII 8580 8585 7 chrIII 8585 8588 6 chrIII 8588 8627 3 chrIII 8627 8655 1
each line with four required fields, they are 1| chromosome/contig ID of the reference sequence, 2| feature start position 3| feature end position and 4| feature coverage score.
thnaks, Vipin T S
On 27 April 2010 19:17, Kanwei Li <kanwei@gmail.com> wrote:
Hi Vipin,
What is a bed wiggle file? We support both, but not at the same time :P
Kanwei
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Kanwei Li -
Vipin TS