User: lhaiyan3

gravatar for lhaiyan3
lhaiyan340
Reputation:
40
Status:
New User
Location:
United States
Last seen:
1 month, 1 week ago
Joined:
4 years, 10 months ago
Email:
l*******@gmail.com

Posts by lhaiyan3

<prev • 37 results • page 1 of 4 • next >
0
votes
0
answers
127
views
0
answers
Comment: C: how to make the correct RNA-seq count file for cnvkit import-rna command?
... Hi, igor: I also tried STAR alinment and then use htseq count for the input files, also failed. Here is my htseq output, ENSG00000000003 0 ENSG00000000005 0 ENSG00000000419 0 ENSG00000000457 0 ENSG00000000460 0 ENSG00000000938 0 ENSG00000000971 0 ENSG00000001036 0 ...
written 5 weeks ago by lhaiyan340 • updated 5 weeks ago by genomax89k
0
votes
0
answers
127
views
0
answers
Comment: C: how to make the correct RNA-seq count file for cnvkit import-rna command?
... this is salmon output, ENST00000631435.1 0.000000 ENST00000415118.1 0.000000 ENST00000434970.2 0.000000 ENST00000448914.1 0.000000 ENST00000632524.1 0.000000 ENST00000633009.1 0.000000 ENST00000634070.1 0.000000 ENST000006329 ...
written 5 weeks ago by lhaiyan340 • updated 5 weeks ago by genomax89k
0
votes
0
answers
127
views
0
answers
how to make the correct RNA-seq count file for cnvkit import-rna command?
... Hi, all: I tried to use the cnvkit import-rna function. I can successfully run the test TCGA dataset, but when I run my own data, I will get wrong message. I used both Samlon and Kallisto to run RNA-seq data and got the 2 column file. My file format is similar with the TCGA test dataset, but I alwa ...
rna-seq written 5 weeks ago by lhaiyan340 • updated 5 weeks ago by genomax89k
0
votes
0
answers
276
views
0
answers
Comment: C: import-rna assertion error
... Hi, Did you find the answer for your problem? I have tried the cnvkit import-rna, similar problem, I have the kallisto 2-column file. I have tested the example TCGA file, no problem. But with my own kallisto input file, there is the wrong message I got, Can anyone please give me some suggestions? T ...
written 5 weeks ago by lhaiyan340
0
votes
0
answers
363
views
0
answers
cnvkit Error message "length of weights should be the same as the number of probes Execution halted"
... Hi, I am using the `CNVkit 0.9.7.b1` for the wgs data. I got the following wrong message: RuntimeError: Subprocess command failed: $ Rscript --vanilla /tmp/tmpg0ig1rdg b'Loading probe coverages into a data frame\nWarning message:\nIn CNA(cbind(tbl$log2), tbl$chromosome, tbl$star ...
cnvkit sequencing written 8 months ago by lhaiyan340 • updated 8 months ago by Medhat8.7k
0
votes
1
answer
610
views
1
answers
Comment: C: Which parameter can be used to set up cutoff not to call peaks <150bp for the ma
... Great. Thanks very much for the information. It works! ...
written 17 months ago by lhaiyan340
3
votes
1
answer
610
views
1
answer
Which parameter can be used to set up cutoff not to call peaks <150bp for the macs2 broad peak calling
... Dear all, I don't want to call peaks <150bp in the `macs2` broadpeak calling. Can you please tell me some suggestions which parameter I can use to set up the cutoff? Thanks very much. best HY ...
macs2 chip-seq written 17 months ago by lhaiyan340 • updated 17 months ago by ATpoint38k
0
votes
1
answer
3.0k
views
1
answers
Comment: C: Tool to annotate ChIP-Seq peaks (hg19 or mm10) and find neighboring peaks from m
... Hi, Abhishek: I tried to use the peak-tool and got the output correctly. But I noticed all the INTERGENICE and ENHANCER, ENHANCER-SUPER did not have the correlate gene, distance to TSS, but the PROMOTER annotation has all this information, did you have way to add these information? Thanks. HY chr ...
written 2.5 years ago by lhaiyan340
0
votes
0
answers
627
views
0
answers
ngsplot-how to get multiplot around the IP peak region and the genes nearest to peak region?
... Dear all, I have the 3 IP (TF1, TF2, TF3) data, and I use mac2 callpeak to get the peak files (TF1.peak). I want to get the multiplot fig about three IP signals at 1, TF1 peak region 2, these IP singals at genes nearest to TF1 peaks . I am not sure what genelist file I should put in the config f ...
chip-seq written 2.6 years ago by lhaiyan340
0
votes
0
answers
1.2k
views
0
answers
How to do the peakcalling for fly spike-in ChIPseq data
... Dear all, We have the fly spike-in ChIP-seq data, I use the following tab to calculate the correlation factor, File/Sample name DMSO_input Induced_Input DMSO_TF1 Induced_TF1 ChIP target TF1 TF1 Treatment DMSO induced DMSO induced Tags mapped to entire dm3 genome 82,362 84,401 2, ...
chip-seq written 2.6 years ago by lhaiyan340 • updated 2.5 years ago by Biostar ♦♦ 20

Latest awards to lhaiyan3

Great Question 8 months ago, created a question with more than 5,000 views. For How to use GSVA for the RNA-seq RPKM file
Popular Question 8 months ago, created a question with more than 1,000 views. For ChrM in the Varscan2 copynumber output
Popular Question 15 months ago, created a question with more than 1,000 views. For ChrM in the Varscan2 copynumber output
Popular Question 15 months ago, created a question with more than 1,000 views. For The plot generated by sciClone
Popular Question 15 months ago, created a question with more than 1,000 views. For only chrM in the varscan2 copynumber output
Popular Question 15 months ago, created a question with more than 1,000 views. For How to analyze the targeted RNA-panel data?
Popular Question 17 months ago, created a question with more than 1,000 views. For ChrM in the Varscan2 copynumber output
Popular Question 2.1 years ago, created a question with more than 1,000 views. For How to build the STAR Genome index from the .gbk file?
Popular Question 2.1 years ago, created a question with more than 1,000 views. For How to use GSVA for the RNA-seq RPKM file
Popular Question 2.1 years ago, created a question with more than 1,000 views. For how to use ESTIMATE to infer tumor purity and stromal score from RNA-seq data?

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 760 users visited in the last hour