User: hkhoja

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hkhoja0
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1 month, 2 weeks ago
Joined:
2 years, 11 months ago
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h*****@covarisinc.com

Posts by hkhoja

<prev • 8 results • page 1 of 1 • next >
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Cutadapt with option of using adapter Fasta file
... Hi, The cutadapt tool available in the galaxy tool shed only allows for the manual input of the adapter sequence, or picking an adapter sequence from the drop down menu one at a time controlled by tab delimited text file. Does anyone have access to a modified wrapper that would allow for using an ...
galaxy written 6 weeks ago by hkhoja0 • updated 6 weeks ago by Jennifer Hillman Jackson23k
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Comment: C: file download very slow
... Thank you Martin. ...
written 22 months ago by hkhoja0
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file download very slow
... Hi. It seems that the bandwidth for downloading of data from galaxy is narrow and the speed very slow(50-100KB/S). Is there another way to download the data from galaxy at a faster rate? FTP? or is there is link to the data which can be used to download the data in another way? Our IT tells us that ...
galaxy written 22 months ago by hkhoja0 • updated 22 months ago by Martin Čech ♦♦ 4.2k
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How to recover a dataset
... Dear administrator.    I accidentally deleted a data file. Is there a way to recover it?  The data set name is 65 FBnew_hg19_groomed_R2  . I have not purged the deleted data yet and cannot figure out how to I delete it.  Thank you for your help hamid           ...
undelet written 22 months ago by hkhoja0 • updated 22 months ago by matthias.desmet130
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collectwgs metrics on galaxy
...   is the picard tool CollectWgsMetrics working now? Thank you.     ...
galaxy tool-error known-issue usegalaxy written 22 months ago by hkhoja0 • updated 22 months ago by Jennifer Hillman Jackson23k
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picard collectwgsmetrics error
...   Hi..I am trying to use the picard collectwgsmetrics on a bam file generated from a whole genome sequencing with a hg38 as the reference sequence. I keep getting the following error; Fatal error: Exit code 1 () Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/galaxy-repl/main/scratch Exception in thread ...
software error written 23 months ago by hkhoja0
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Answer: A: Need help with "Sort" tool
... Thank you Bjoern and Jennifer for your input. to explain further, I needed to sort the bam file so that it could be used for a few of the picard analysis tools. IGV also requires sorted bam files. I was not sure if the sort tool on galaxy was the correct one to use since my data is already there.  I ...
written 3.0 years ago by hkhoja0
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Need help with "Sort" tool
...   Hi Can this tool available on Galaxy be used to sort a sam file before converting to bam file?  Should the default settings be used for that or do i need to identify the columns? Thank you         Tool name: Sort Tool version: 1.0.3 Tool ID: sort1   ...
sort written 3.0 years ago by hkhoja0

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