User: jonessara770

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jonessara770100
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Posts by jonessara770

<prev • 52 results • page 1 of 6 • next >
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Comment: C: How can I download the fasta file of RepeatMasker UCSC table directly?
... Yes, I did and I save the file but it is truncated from chr18 upwards. ...
written 18 days ago by jonessara770100
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Comment: C: How can I download the fasta file of RepeatMasker UCSC table directly?
... Thanks! I tied this but the file is truncated. ...
written 18 days ago by jonessara770100
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How can I download the fasta file of RepeatMasker UCSC table directly?
... Hi, I am a newbie in Retrotransposable/repeat elements analysis. I used UCSC table in order to get the sequence of RepeatMasker table in fasta format. When I download it through the webpage, the file is truncated at chr16 and does not have all chromosome. How can I download the fastq file of R ...
te repeat retrotransposable/repeat written 19 days ago by jonessara770100
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Comment: C: interpretation of intronic variant detected by WES
... Thank Kevin, The tools in your previous post are for predicting if a variant affects splicing. right? I did this step before and I know it affects splicing but I don't know how to check if it produces truncating protein. ...
written 24 days ago by jonessara770100
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interpretation of intronic variant detected by WES
... Hi I detected a variant in the intron of a gene that is predicted by MutationFinder to affect splicing by activation of an intronic cryptic acceptor site. What is the method to check if this variant produces truncating proteins or not? btw, my data is WES. Thanks Sara ...
wes written 25 days ago by jonessara770100
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what is the volumn of data on GDC?
... Hi How can I find how much data are on GDC portal for all cancer types and samples? or is there any statistic for the volume of NGS data generated in cancer so far? Thanks S ...
next-gen written 10 weeks ago by jonessara770100 • updated 10 weeks ago by Kevin Blighe25k
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How to take in consideration UMI in WES pipeline?
... Hi I have received WES data treated with SureSelectXT HS Reagent that has UMI. I wonder how I should do the analysis for this? what I should change in my WES pipeline to consider this? is there any tutorial for analyzing WES with UMI? could you please share your experiences? Thanks Sara ...
wes written 11 weeks ago by jonessara770100 • updated 11 weeks ago by i.sudbery2.4k
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errors in newCellDataSet Monocle function
... Hi I am newbie in using Monocle. Would you please help me with this error? The author said I should not use as.matrix for sparse matrix but the function will not work otherwise. HSMM <- newCellDataSet(as(expr_matrix, "sparseMatrix"), phenoData = pd1, featureData = fd1, expressionFamily=negbi ...
single cell rna-seq written 3 months ago by jonessara770100 • updated 12 weeks ago by Batu40
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Answer: C: grabix installation from github
... Ok I unloaded module file gcc-4.9.3 and run 'make' it and it create grabix ...
written 4 months ago by jonessara770100
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Comment: C: grabix installation from github
... CentOS6/software/gcc/gcc-4.9.3/bin/gcc ...
written 4 months ago by jonessara770100

Latest awards to jonessara770

Popular Question 18 days ago, created a question with more than 1,000 views. For extract sequence around snp
Student 24 days ago, asked a question with at least 3 up-votes. For How to systematically check if a bam file is truncated
Popular Question 3 months ago, created a question with more than 1,000 views. For ExAC PLI score calculation
Scholar 4 months ago, created an answer that has been accepted. For C: grabix installation from github
Popular Question 5 months ago, created a question with more than 1,000 views. For How to systematically check if a bam file is truncated
Popular Question 11 months ago, created a question with more than 1,000 views. For ExAC PLI score calculation
Popular Question 11 months ago, created a question with more than 1,000 views. For How to systematically check if a bam file is truncated

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