User: Lilach F

gravatar for Lilach F
Lilach F190
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190
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New User
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Last seen:
5 years, 6 months ago
Joined:
6 years, 4 months ago
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l*******@gmail.com

Posts by Lilach F

<prev • 19 results • page 1 of 2 • next >
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Comment: C: Problem With Depth Of Coverage On Bam Files (Gatk Tools)
... May I join to the question of Carlos? what is exactly hg_g1k_v37? and how can I get the intervals of specific genes in this format? Thanks, Lilach 2012/6/27 Lilach Friedman ...
written 5.6 years ago by Lilach F190
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Comment: C: Problem With Depth Of Coverage On Bam Files (Gatk Tools)
... Hi Jennifer, Is there a way to directly upload my files from the public Galaxy to my cloud Galaxy instance (in AWS)? Or should I download them first to my computer, and then to upload them? (It takes a lot of time because of the low uploading speed). Thanks, Lilach 2012/6/26 Jennifer Jackson ...
written 5.6 years ago by Lilach F190
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Comment: C: Problem With Depth Of Coverage On Bam Files (Gatk Tools)
... Hi Carlos, Thank you very much for this explanation. The format of my intervals file is: chr133289059732890664NM_000059_cds_1_0_chr13_32890598_f0+chr1332893213 32893462NM_000059_cds_2_0_chr13_32893214_f0+chr133289921232899321 NM_000059_cds_3_0_chr13_32899213_f0+chr133290023732900287 NM_000059_cds_ ...
written 5.6 years ago by Lilach F190
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Comment: C: Problem With Depth Of Coverage On Bam Files (Gatk Tools)
... Hi Jennifer, Thank you for this reply. I made a new BWA file, this time using the hg19(full) genome. However, when I am trying to use DepthOfCoverage, the reference genomr is stucked on the hg_g1k_v37 (this is the only option to select), and I cannot change it to hg19(full). Most probably, because ...
written 5.6 years ago by Lilach F190
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Comment: C: Generate Pileup Not Working?
... Hi Jen, Thank you! It worked on the original BWA, only when it is aligned to hg19 (failed when the alignment was to hg_g1k_v37. However, it doen't work on BAM or SAM files after sorting with Select Matching pattern: XT:A:U or after filtering the BWA results with Filter SAM on bitwise flag values. ...
written 5.6 years ago by Lilach F190
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Problem With Depth Of Coverage On Bam Files (Gatk Tools)
... Hi, I am trying to used Depth of Coverage to see the coverages is specific intervals. The intervals were taken from UCSC (exons of 2 genes), loaded to Galaxy and the file type was changed to intervals. I gave to Depth of Coverage two BAM files (resulted from BWA, selection of only raws with the Mat ...
alignment bwa written 5.6 years ago by Lilach F190 • updated 5.6 years ago by Jennifer Hillman Jackson23k
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Generate Pileup Not Working?
... Hi, I am trying to do variants call with "generate pileup". My steps where: 1. BWA 2. select only lines with the pattern Matching pattern: XT:A:U 3. SAM-to-BAM 4. then I tried to use "Generate pileupfrom BAM dataset" However, it does not work, and I get the error message: 114: Generate pileup on d ...
bam samtools alignment bwa written 5.6 years ago by Lilach F190 • updated 5.6 years ago by Jennifer Hillman Jackson23k
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Comment: C: Galaxy In Aws Ami
... Hi Dannon and Enis, I succeeded to enter cloudman today. Thanks for fixing the bug! Lilach 2012/6/14 Dannon Baker ...
written 5.6 years ago by Lilach F190
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Answer: A: Galaxy + Sge
... and I terminated a created from the beginning new instanced for the last several hours (at least 5 different instances). All don't work. Lilach 2012/6/14 Lilach Friedman ...
written 5.6 years ago by Lilach F190
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Galaxy In Aws Ami
... Hi, Can somebody please help me? I'm trying for hours to connect to Galaxy on Amazon EC2. I did everything according the instructions, but did not succeed. The "Access Galaxy" button in the instance remains grey out. I copied the screen print and the log to the attached file. Can anyone help me plea ...
galaxy written 5.6 years ago by Lilach F190 • updated 5.6 years ago by Dannon Baker3.7k

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