User: djuna.gulliver

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Posts by djuna.gulliver

<prev • 14 results • page 1 of 2 • next >
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Delete data from MG-RAST
... Is there a way to delete completed jobs from MG-RAST? For some reason, a couple of my jobs were uploaded as amplicon, when they were actually WGS, and I need to re-upload them. It would be nice to delete the incorrectly uploaded sequences so they don't just sit useless in my data profile. I have ...
mg-rast written 3 months ago by djuna.gulliver0
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Answer: A: Different Problems with Velvet
... You can make this work on Velvet.  I struggle too (and ask many questions on Biostar), but I managed to assemble my metagenome with various KMER lengths of 21, 31, and 41. Might I suggest also inputting "-short" in the velveth command?  So it would be: velveth out-dir 17 -short -fastq /path/to/th ...
written 2.2 years ago by djuna.gulliver0
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Answer: A: Question: How do I change the fasta format from CLC Workbench for MG-RAST
... Got it! sed 's/ Average coverage: /_[cov=/g' BG.fa | sed 's/[0-9].[0-9][0-9]*/&]/g' >BGcon.fa That took way longer for me to figure out than I'll ever admit to my supervisor. Well, my day can only go downhill from here, I should just call it a day. ...
written 2.2 years ago by djuna.gulliver0
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Comment: C: Question: How do I change the fasta format from CLC Workbench for MG-RAST
... It's getting much closer. Both the awk language suggestion and the sed language suggestion resulted in the "]" being placed in the correct spot, but the fist line of sequence is then tagged on the end of the header.  So it looks like: >sequence_1_[cov=5.6]ACCAGCGTTCTCTACACA ATTACACGGCACCCAC > ...
written 2.2 years ago by djuna.gulliver0
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Comment: C: Question: How do I change the fasta format from CLC Workbench for MG-RAST
... It's getting much closer. Both the awk language suggestion and the sed language suggestion resulted in the "]" being placed in the correct spot, but the fist line of sequence is then tagged on the end of the header.  So it looks like: >sequence_1_[cov=5.6]ACCAGCGTTCTCTACACA ATTACACGGCACCCAC > ...
written 2.2 years ago by djuna.gulliver0
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Question: How do I change the fasta format from CLC Workbench for MG-RAST
... I'm using a trial of CLC Workbench for assemblies. I would like to enter my assembled fa files into MG-RAST.  However, CLC Workbench gives files in the form of: >sequence_1 Average coverage: 5.6 ACCAGCGTTCTCTACACA >sequence_2 Average coverage: 6.4 GTTATACAGGATAAGAATC And so forth (of course ...
assembly written 2.2 years ago by djuna.gulliver0
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Comment: C: Question: Can't change MAXKMERLENGTH on Velvet
... Thanks. I compiled the zlib with: ./configure --prefix=/gullived/home (which is the folder I want zlib in) make make install After I put in the LD_FLAGS and CDD_FLAGS, it appeared to work.  So it was a zlib issue after all. ...
written 2.3 years ago by djuna.gulliver0
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Comment: C: Question: Can't change MAXKMERLENGTH on Velvet
... Yes, after that message, it says: compilation terminated. make: ***[obj/readSet.o] Error 1 I have just now tried to download a new zlib (version 1.2.8).  I run the commands: PATH=$PATH:zlib-1.2.8 (which is the pathway to my zlib folder) cd velvet_1.2.10 make MAXKMERLENGTH=71 But I still get th ...
written 2.3 years ago by djuna.gulliver0 • updated 2.3 years ago by Ram11k
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Comment: C: Question: Can't change MAXKMERLENGTH on Velvet
... Perhaps the problem can be deduced by the following error message whenever I run a make command: src/readSet.c:36:18: fatal error: zlib.h: No such file or directory #include <zlib.h> Whatever that means. ...
written 2.3 years ago by djuna.gulliver0 • updated 2.3 years ago by Ram11k
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Comment: C: Question: Can't change MAXKMERLENGTH on Velvet
... Sorry, it was suppose to say 1.2.10 for all of the versions. This is why my New Years Resolution is to reread every email and post for typo's before hitting that send button. ...
written 2.3 years ago by djuna.gulliver0

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Popular Question 2.2 years ago, created a question with more than 1,000 views. For Question: Can't change MAXKMERLENGTH on Velvet

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