Forum: Bioinformatics
Yesterday, 03:45 PM
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Replies: 218
Views: 66,349
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Forum: General
02-19-2019, 05:41 PM
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Replies: 5
Views: 274
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Forum: RNA Sequencing
02-19-2019, 12:48 PM
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Replies: 2
Views: 113
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Forum: Epigenetics
02-19-2019, 10:35 AM
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Replies: 1
Views: 99
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Forum: RNA Sequencing
02-19-2019, 10:34 AM
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Replies: 5
Views: 107
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Forum: RNA Sequencing
02-19-2019, 10:15 AM
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Replies: 5
Views: 107
Oops. I should have looked at the error...
Oops. I should have looked at the error carefully. You are correct.
Edit: Found the problem. You have a space between clipped and file name here (clipped/ SRR359063_2.fastq.zip ). Remove that.
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Forum: RNA Sequencing
02-19-2019, 09:57 AM
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Replies: 5
Views: 107
STAR requires a lot of RAM depending on genome...
STAR requires a lot of RAM depending on genome size. e.g. human genome will need ~30G of free RAM which you may not have available on your Mac. If that is true, you will not be able to do this on...
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Forum: General
02-19-2019, 06:31 AM
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Replies: 5
Views: 274
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Forum: RNA Sequencing
02-18-2019, 04:57 PM
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Replies: 2
Views: 118
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Forum: Bioinformatics
02-18-2019, 04:39 AM
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Replies: 93
Views: 18,205
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Forum: RNA Sequencing
02-14-2019, 02:13 PM
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Replies: 2
Views: 244
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Forum: Bioinformatics
02-14-2019, 06:50 AM
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Replies: 31
Views: 18,434
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Forum: Bioinformatics
02-13-2019, 04:34 PM
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Replies: 1
Views: 161
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Forum: RNA Sequencing
02-13-2019, 04:29 PM
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Replies: 4
Views: 194
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Forum: RNA Sequencing
02-13-2019, 12:45 PM
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Replies: 4
Views: 194
The directory you have the program "fastq-dump"...
The directory you have the program "fastq-dump" is likely not in your $PATH ( a set of directories that are automatically searched when you try to run something). You could try ./fastq-dump if the...
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Forum: Bioinformatics
02-12-2019, 12:40 PM
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Replies: 8
Views: 251
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Forum: Bioinformatics
02-12-2019, 10:09 AM
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Replies: 8
Views: 251
Can you validate your fastq files to make sure...
Can you validate your fastq files to make sure there are no errors in the file?
Use validateFiles (http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/validateFiles)from Kent Utilities (UCSC)....
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Forum: Bioinformatics
02-11-2019, 03:20 PM
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Replies: 8
Views: 251
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Forum: Bioinformatics
02-11-2019, 12:26 PM
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Replies: 8
Views: 251
Do you get an error right away or does the...
Do you get an error right away or does the program run for some time?
Are these bbmerged reads? Wonder if you should try to do the binning with original fastq data. Is that a possibility?
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Forum: Bioinformatics
02-11-2019, 12:23 PM
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Replies: 1
Views: 228
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Forum: Bioinformatics
02-10-2019, 04:59 PM
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Replies: 1
Views: 190
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Forum: Bioinformatics
02-07-2019, 04:46 AM
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Replies: 320
Views: 95,727
We are making progress!
How much memory do...
We are making progress!
How much memory do you have on this Mac? I suggest using 85% of the maximum memory you have available with BBTools. You also need to specify "in1= and out1=" to go with...
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Forum: Bioinformatics
02-06-2019, 09:31 AM
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Replies: 320
Views: 95,727
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Forum: Bioinformatics
02-06-2019, 05:52 AM
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Replies: 320
Views: 95,727
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Forum: Sample Prep / Library Generation
02-01-2019, 04:00 AM
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Replies: 8
Views: 1,359
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