User: Z-F

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Z-F20
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8 years, 6 months ago
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z*********@yahoo.com

Posts by Z-F

<prev • 14 results • page 1 of 2 • next >
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Comment: C: GermlineCNVCaller- Interval scattering for WES data
... Yes, I actually skipped the scattering step. As far as I understood, GATK says that this scattering only helps in improving speed and the need for larger memory. I just did not scatter the intervals and simply used the exome interval file, I had prepared according to their recommendations. Now, i ...
written 10 days ago by Z-F20
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Comment: C: GermlineCNVCaller- Interval scattering for WES data
... Thanks for the reply. To be more clear, I actually determined an interval in my command and it seems that it will calculate the CNVs according to the exome interval file I have provided (33Mbp). The point is, as far as I understood, GATK tutorial says this step needs a lot of memory, and to preve ...
written 10 days ago by Z-F20
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GermlineCNVCaller- Interval scattering for WES data
... Hi everyone, I am working with the gCNV pipeline using 200 WES samples to make the cohort ploidy model first. Following [this][1] tutorial, I am now trying to call copy numbers using GermlineCNVCaller. In part 4.2, I could find some guides into how to provide interval lists for scattering. I am s ...
gatk wes germlinecnvcaller cnv written 10 days ago by Z-F20
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Comment: C: GATK GermlineCNVCaller & PostprocessGermlineCNVCalls
... Thanks! That solved the issue. ...
written 4 weeks ago by Z-F20
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Answer: A: GATK GermlineCNVCaller & PostprocessGermlineCNVCalls
... Hi everyone, I am trying to use the CNV caller. a) GATK version used: gatk-4.1.4.0 I used the following command in this step. > ../gatk-4.1.4.0/gatk -L > Filtered_annotated_preprocessed_intervals_Twist.interval_list > --interval-merging-rule OVERLAPPING_ONLY -I S1071Nr10.counts.hdf5 -I S ...
written 6 months ago by Z-F20
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Comment: A: An error when using ENCODE-Phantompeakqualtools
... The operating system which I ma working is Linux 14.04. At the end, I found that I should install gawk and then it worked properly. Thanks .. ...
written 3.8 years ago by Z-F20
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An error when using ENCODE-Phantompeakqualtools
... Dear All, I am a newbie in ChIP-seq analysis and now I am trying to assess NSC/RSC values using "phantompeakqualtools", but unfortunately I got an error and cant find any similar posts for that. Would you please help me ! I used this command to determine strand cross-correlation peak: Rscript /da ...
nsc R awk chip-seq rsc written 3.9 years ago by Z-F20
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Comment: C: ChIP seq- input DNA control for normalization
... Dear jotan, Thanks, I think we should sequence the "input DNA" as all of you mentioned. Thanks for the reply. ...
written 4.4 years ago by Z-F20
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Comment: C: ChIP seq- input DNA control for normalization
... Dear Michele, Thanks for your comprehensive reply. It helped a lot. ...
written 4.4 years ago by Z-F20
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Comment: C: ChIP seq- input DNA control for normalization
... Dear John, Thanks for your reply. Actually, the problem is that I am going to sonicate three similar HEK293 cell lines which are all transfected with a same gene but in WT and mutant forms and for all of these I only use one antibody (anti-GFP). Can I still use one "input DNA'' for all 3 samples (3 ...
written 4.4 years ago by Z-F20

Latest awards to Z-F

Great Question 3.7 years ago, created a question with more than 5,000 views. For ChIP seq- input DNA control for normalization
Popular Question 3.7 years ago, created a question with more than 1,000 views. For ChIP seq- input DNA control for normalization
Popular Question 3.7 years ago, created a question with more than 1,000 views. For Analysis Of The Genotyping Data
Popular Question 7.7 years ago, created a question with more than 1,000 views. For Analysis Of The Genotyping Data
Popular Question 7.7 years ago, created a question with more than 1,000 views. For Segmentation Fault (Core Dumped)-Bwa Indexing Ref Genome

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