User: Lisa

gravatar for Lisa
Lisa20
Reputation:
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Status:
New User
Location:
Pakistan
Last seen:
3 years, 11 months ago
Joined:
4 years, 4 months ago
Email:
l**************@126.com

Posts by Lisa

<prev • 9 results • page 1 of 1 • next >
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Comment: C: How to extract the peptide sequence centered the amino acid position of protein?
... I've solved this problem. ...
written 4.3 years ago by Lisa20
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Comment: C: How to extract the peptide sequence centered the amino acid position of protein?
... Yes, I have the chromosome and the protein position information like: chr1 230 What I want to extract is the amino acid sequence centered the chr1:230 position, with one length parameter offered L. So the actual peptide sequence is the 230-L to 230+L region on chr1. If there is any program would a ...
written 4.3 years ago by Lisa20
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How to extract the peptide sequence centered the amino acid position of protein?
... Hi, can any tools be able to extract the peptide sequence, in a certain length, centered the amino acid position of protein? Thanks. ...
peptide sequence;amino acid position written 4.3 years ago by Lisa20
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Comment: C: sciClone error for two sample
... I think there are some problems with my copy-number data. I'll try and adjust again in the CNA calling and then try sciclone again. ...
written 4.4 years ago by Lisa20
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Comment: C: sciClone error for two sample
... OK, thank you. So if I pre-filter those copy-number amplified and deleted regions and only maintain the neutral regions to feed sciClone, can that way be fine? ...
written 4.4 years ago by Lisa20
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Comment: C: sciClone error for two sample
... Do you have readcounts for each site in both tumors? The first two columns of the lists of variants that you feed in should be identical. Do you mean I have to merge the chromosome position of the two samples? For example: tumor1: chr1 100 8 6 42.8571 chr1 156 12 3 20.0000 ... tumor2: chr1 1 ...
written 4.4 years ago by Lisa20
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Comment: C: sciClone input, output and parameters
... Hi Chris, I post the question at https://www.biostars.org/p/118083/ Thanks. ...
written 4.4 years ago by Lisa20
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sciClone error for two sample
... I'm having a try with sciClone for my exome-seq data. It work fine in the one-sample running but an error reported when using two samples (tumors from two different individuals) for comparison. I use the SNV and CNA information. The SNV file format:  contig position t_ref_count t_alt_count tumor ...
cna sciclone snv written 4.4 years ago by Lisa20 • updated 4.4 years ago by Chris Miller20k
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Comment: C: sciClone input, output and parameters
... When using one sample, sciclone just work fine. But when tring two samples comparison, an error warning generated: [1] "checking input data..." [1] "Not all variants fall within a provided copy number region. The copy number of these variants is assumed to be 2." [1] "Not all variants fall within a ...
written 4.4 years ago by Lisa20

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