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Forum: Bioinformatics 01-22-2018, 11:55 AM
Replies: 5
Views: 1,167
Posted By j.cappellazzi
Thanks neavemj! That was perfect. All of the...

Thanks neavemj! That was perfect. All of the files are now renamed. I will keep going on these practice files to make sure all is well, but I think that's exactly what I wanted :-). I need to take a...
Forum: Bioinformatics 01-21-2018, 12:20 PM
Replies: 5
Views: 1,167
Posted By j.cappellazzi
Thanks for the quick response kmcarr. I forgot to...

Thanks for the quick response kmcarr. I forgot to mention another step in the pipeline in my first post. Before I run multiple_split_libraries_fastq.py, I would like to run count_seqs.py as well as...
Forum: Bioinformatics 01-19-2018, 04:12 PM
Replies: 5
Views: 1,167
Posted By j.cappellazzi
Question Qiime Ubuntu Command Line File Name Code?

After running multiple_join_paired_ends.py on my 600 Illumina MiSeq files, the output leaves each sample in individual folders. The folder has a unique name, but all of the files in each subdirectory...
Forum: Bioinformatics 08-02-2017, 12:51 PM
Replies: 16
Views: 2,745
Posted By j.cappellazzi
It worked!

Well, now I understand my coding limitations. I didn't know the "./" meant I needed to provide the path to the output folder. I messed around with the code and did...
...
Forum: Bioinformatics 08-02-2017, 11:39 AM
Replies: 16
Views: 2,745
Posted By j.cappellazzi
@neavemj I also tried the code you suggested...

@neavemj

I also tried the code you suggested after getting into the proper directory at the command line and fixing the "-i" issue...
...
Forum: Bioinformatics 08-02-2017, 11:25 AM
Replies: 16
Views: 2,745
Posted By j.cappellazzi
@Genomax @neavemj Well, that was frustrating...

@Genomax @neavemj

Well, that was frustrating and silly. It wasn't recognizing the -i because it was a long "-" not a short one. Must have been from copying from word into the command line. WOW!
...
Forum: Bioinformatics 08-01-2017, 05:58 PM
Replies: 16
Views: 2,745
Posted By j.cappellazzi
If you can see something wrong, here is the...

If you can see something wrong, here is the .fastq file. I couldn't figure out how to post it, so just delete .pdf from the end (I think that will work).
Forum: Bioinformatics 08-01-2017, 05:53 PM
Replies: 16
Views: 2,745
Posted By j.cappellazzi
neavemj - same story with the code you posted....

neavemj - same story with the code you posted. Thanks.
Forum: Bioinformatics 08-01-2017, 05:48 PM
Replies: 16
Views: 2,745
Posted By j.cappellazzi
I just loaded the fastQValidator and pulled a...

I just loaded the fastQValidator and pulled a subsample out of my original folder. I checked 43 .fastq files with fastQValidator and they all passed with the following result...
...
Forum: Bioinformatics 08-01-2017, 01:56 PM
Replies: 16
Views: 2,745
Posted By j.cappellazzi
Okay, thanks for the clarification. Now I'm...

Okay, thanks for the clarification. Now I'm getting the following when I put in the two commands...

fastq_quality_filter: input file (-) has unknown file format (not FASTA or FASTQ), first...
Forum: Bioinformatics 08-01-2017, 10:06 AM
Replies: 16
Views: 2,745
Posted By j.cappellazzi
Thanks. Quick follow up... should I be pasting...

Thanks. Quick follow up... should I be pasting the entirety of the code as written? The coding language I don't understand is the "for i in 'ls -1" etc.

Is this all one command?

Thanks.
Forum: Bioinformatics 08-01-2017, 09:29 AM
Replies: 16
Views: 2,745
Posted By j.cappellazzi
Fastx-Toolkit - Analyze multiple files in directory (Linux/Qiime)

I am trying to run the fastq_quality_filter on a directory of .fastq files (~500) where each file has a unique name. I simply cannot get it to work on the Linux Command Line within the Qiime...
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