User: zhhxu9
zhhxu9 • 0
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- 3 years, 11 months ago
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Posts by zhhxu9
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... Because I am analysing the ChIP-Seq data. I want to find the consensus motif bind by transcription factor around peak summit . However the summit I got is only the start coordinates in .BED format. Here is what I did:
Firstly, use excel (idea comes from Bjoern) to get the specific scope around th ...
written 4.0 years ago by
zhhxu9 • 0
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... Hi,
I think I find out a way to solve this problem. Thanks for your advise.
Zhenhua
...
written 4.0 years ago by
zhhxu9 • 0
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... Hi,
But I do not have any sequence now. All I have are start coordinates. For example, Chr1: 68029345. And I have thousand of them. What I want is to find the coordinates on a specific genome and extract 100bp genome sequence around the start coordinate (50bp upstream, 50bp downstream). Any suggest ...
written 4.0 years ago by
zhhxu9 • 0
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... Hello everyone,
I have some genome coordinates with only the start site. I want to extract 50bp of the genome sequence of both upstream and down stream from this start coordinate. Anyone happen to know what tool can fulfil this job? Either on Galaxy on not. Thanks a lot.
Zhenhua
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written 4.0 years ago by
zhhxu9 • 0
• updated
4.0 years ago by
Bjoern Gruening ♦ 5.1k
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... Hi Jennifer,
When I try to use the workflow, do I have to input the raw data? Because I only have the data which has been trimmed for low quality and adaptor sequence. So I do not have the raw data. Under the first two droplist, there is no blank to be selected. Any idea about this? Thanks.
Zhenhu ...
written 4.1 years ago by
zhhxu9 • 0
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... Thanks Jennifer, I appreciate your kind help. I will try to use the new tool you provided.
...
written 4.1 years ago by
zhhxu9 • 0
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... Thanks Bjoern, I will take a shot.
...
written 4.1 years ago by
zhhxu9 • 0
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... Hi,
I would like to know if there is any tool can do the following job?
I have some data files in fastq format generating from paired -end sequencing. the reads have been generally trimmed to remove the low quality reads and adaptor contaminations. But the R1 and R2 files do not have equal number ...
written 4.1 years ago by
zhhxu9 • 0
• updated
4.1 years ago by
Jennifer Hillman Jackson ♦ 25k
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... Hi,
I am analysing my ChIP-Seq data which generated by paired-end sequencing. But due to some experimental issues. It is better to mapping both the R1 and R2 data in single-end way separately.
So I would like to know how can I combine two SAM or BAM files into one file and how can I get the mappin ...
written 4.1 years ago by
zhhxu9 • 0
• updated
4.1 years ago by
Bjoern Gruening ♦ 5.1k
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