User: jonessara770

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jonessara77040
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Posts by jonessara770

<prev • 40 results • page 1 of 4 • next >
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Comment: C: What are the step for germline analysis with CNVKit?
... No, I would like to try some of them and compare the results. XHMM installation is very difficult! ...
written 9 days ago by jonessara77040
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What are the step for germline analysis with CNVKit?
... Hello, I would like to call CNV on germline samples with CNVKit. the documentation for CNV calling from germline is a bit confusing. could you please give me a step by step instruction to run CNVkit on germline WES data? Thanks sara ...
whole exome sequneing written 9 days ago by jonessara77040
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Comment: C: best and easy Germline CNV caller with WES
... Thanks! isn't it difficult to run? ...
written 9 days ago by jonessara77040
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best and easy Germline CNV caller with WES
... Hi all, I would like to check the presence of germline CNV in my samples. I wonder what are the best germline CNV callers using WES data ? Please share your experiances Thanks in advance Sara ...
whole exome seq written 9 days ago by jonessara77040
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counts reads for miRNA mapped againt mirbase
... Hello, I aligned my miRNA-Seq againt mirbase by bowtie. I would like to count the reads aligned to each miRNA. is there any tools specific for this ? Thanks ...
mirna-seq written 16 days ago by jonessara77040
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Comment: C: Converting TCGA Bam files to fastq: Picard does not work!
... yes, these are aligned by BWA meme ...
written 6 months ago by jonessara77040
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Comment: C: Converting TCGA Bam files to fastq: Picard does not work!
... Thanks for your reply! I ran it again with this version (picard-2.9.0/picard.jar SamToFastq VALIDATION_STRINGENCY=LENIENT) but get the same error. ...
written 6 months ago by jonessara77040
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Converting TCGA Bam files to fastq: Picard does not work!
... Hello, I am trying to convert bam files from TCGA to fastq. Picard gives the following error: picard.sam.SamToFastq done. Elapsed time: 0.78 minutes. Runtime.totalMemory()=2058354688 To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Exception in threa ...
wes sequencing written 6 months ago by jonessara77040 • updated 6 months ago by Pierre Lindenbaum104k
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(Closed) draw gene on chromosome
... Hi, I wonder how can I plot gene names on chromosomes like example below? Thanks ![enter image description here][1] [1]: http://www.nature.com/nature/journal/v505/n7483/images/nature12981-f1.jpg ...
gene written 9 months ago by jonessara77040
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Comment: C: duplicate read names in TCGA raw bam file
... No there are there. this is output of bedtools bamtofastq fastq1 @C0UL8ACXX120727:8:2301:17486:13986/1 @C0UL8ACXX120727:8:2301:17486:13986/1 fastq2 @C0UL8ACXX120727:8:2301:17486:13986/2 @C0UL8ACXX120727:8:2301:17486:13986/2 ...
written 9 months ago by jonessara77040

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Popular Question 5 months ago, created a question with more than 1,000 views. For ExAC PLI score calculation
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

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