Eel pond mRNAseq tutorial #2
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| like so:: | ||
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| cd /mnt/work | ||
| python /usr/local/share/khmer/sandbox/write-trimmomatic.py > trim.sh |
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A script that... writes another script? This can be useful, but it's not common practice.
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See https://github.com/ged-lab/khmer/blob/bleeding-edge/sandbox/write-trimmomatic.py for the script source.
Yeah, I struggled with this for a while. It seemed easier to write it in Python... but that was before I invested in all the other shell stuff below. Sigh.
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| And, finally, you can toss the pe.fq.gz files, because you've turned *those* | ||
| into .pe and .se files. | ||
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Add :: so "rm *.pe.qc.fq.gz" shows up as code
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This is done in the latest version, right?
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In doc/mrnaseq/1-quality.txt:
+Yikes! What to do?
+
+Well, first, you can get rid of the original data. You already have it on a
+disk somewhere, right? ::
+
- rm *.fastq.gz
+Next, you can get rid of the 'pe.fq.gz' and 'se.fq.gz' files, since you
+only want the QC files. So::
+
- rm _.pe.fq.gz *.se.fq.gz
+And, finally, you can toss the pe.fq.gz files, because you've turned *those_
+into .pe and .se files.
+
This is done in the latest version, right?
Nope still just a white space with an indentŠ
‹
Reply to this email directly or view it on GitHub
https://github.com/ngs-docs/edda/pull/2/files#r5820320 .
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fixed! (in the khmer-protocols version)
On Fri, Aug 16, 2013 at 03:12:06PM -0700, LSheneman wrote:
+Yikes! What to do?
+
+Well, first, you can get rid of the original data. You already have it on a
+disk somewhere, right? ::
+
- rm *.fastq.gz
+Next, you can get rid of the 'pe.fq.gz' and 'se.fq.gz' files, since you
+only want the QC files. So::
+
- rm _.pe.fq.gz *.se.fq.gz
+And, finally, you can toss the pe.fq.gz files, because you've turned *those_
+into .pe and .se files.
+In doc/mrnaseq/1-quality.txt:
+Yikes! What to do?
+
+Well, first, you can get rid of the original data. You already have it on a
+disk somewhere, right? ::
+
- rm *.fastq.gz
+Next, you can get rid of the 'pe.fq.gz' and 'se.fq.gz' files, since you
+only want the QC files. So::
+
- rm _.pe.fq.gz *.se.fq.gz
+And, finally, you can toss the pe.fq.gz files, because you've turned *those_
+into .pe and .se files.
+
This is done in the latest version, right?Nope still just a white space with an indent??
???
Reply to this email directly or view it on GitHub
https://github.com/ngs-docs/edda/pull/2/files#r5820320 .
Reply to this email directly or view it on GitHub:
https://github.com/ngs-docs/edda/pull/2/files#r5826092
C. Titus Brown, [email protected]
Instructions referred curl, but the command used was wget. Fix correct flag (should be -o instead of -O).
Fix instruction for download
add warnings about content not being maintained
one more warning
No description provided.