Forum: Bioinformatics
08-11-2016, 05:46 AM
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Replies: 4
Views: 1,875
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Forum: Bioinformatics
08-04-2016, 05:09 AM
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Replies: 4
Views: 1,875
I was going to point you to...
I was going to point you to http://www.ebi.ac.uk/ena/data/view/SRR1168519 and suggest downloading the 'Submitted files (ftp)', but there are none. I have two alternative solutions left:
- try to...
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Forum: Bioinformatics
05-05-2016, 01:56 AM
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Replies: 6
Views: 1,367
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Forum: Bioinformatics
11-17-2015, 11:37 PM
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Replies: 4
Views: 2,249
I would have a look at...
I would have a look at https://github.com/PacificBiosciences/Bioinformatics-Training/wiki/Large-Genome-Assembly-with-PacBio-Long-Reads, which has many suggestions.
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Forum: Bioinformatics
11-06-2015, 12:23 PM
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Replies: 1
Views: 852
Does this help (a bit)?...
Does this help (a bit)? https://contig.wordpress.com/2010/03/11/newbler-output-i-the-454newblermetrics-txt-file/#comment-91
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Forum: Bioinformatics
10-16-2015, 05:38 AM
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Replies: 4
Views: 3,109
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Forum: Bioinformatics
09-28-2015, 07:37 AM
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Replies: 12
Views: 2,155
The page you mention contains the default...
The page you mention contains the default settings, yes. Unfortunately, you can't get these from the log files.
However, I agree with @maubp that the reviewer's request is nonsensical. What is...
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Forum: 454 Pyrosequencing
09-16-2015, 05:55 AM
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Replies: 3
Views: 6,508
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Forum: 454 Pyrosequencing
09-15-2015, 05:03 AM
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Replies: 3
Views: 6,508
Primers should already be removed, both the...
Primers should already be removed, both the primers that are used for sequencing and the MID sequences. When in doubt, you could use prinseq, it will try to detect adaptor sequences....
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Forum: 454 Pyrosequencing
08-04-2015, 02:40 AM
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Replies: 3
Views: 6,325
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Forum: 454 Pyrosequencing
07-02-2015, 04:50 AM
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Replies: 3
Views: 6,325
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Forum: Bioinformatics
05-13-2015, 06:22 AM
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Replies: 1
Views: 1,186
Newbler determines pair based on the sequence...
Newbler determines pair based on the sequence ID's. I think it does not matter whether the reads are interleaved or not. But you need to check the 454PairStatus file(s) to be sure.
Maybe. Get...
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Forum: Bioinformatics
05-07-2015, 11:45 PM
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Replies: 9
Views: 3,797
(this answers some of the previous posts).
...
(this answers some of the previous posts).
You already seem to have a very good assembly. I recommend trying Pilon http://www.broadinstitute.org/software/pilon/ to polish your assembly and...
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Forum: Bioinformatics
02-25-2015, 07:12 AM
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Replies: 3
Views: 1,380
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Forum: De novo discovery
02-18-2015, 07:00 AM
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Replies: 4
Views: 4,765
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Forum: Pacific Biosciences
02-16-2015, 02:53 AM
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Replies: 4
Views: 3,973
You could also use PBcR...
You could also use PBcR wgs-assembler.sourceforge.net/wiki/index.php?title=PBcR for steps 1-5, and then smrtanalysis from the command line for quiver. I hardly ever use the portal...
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Forum: Pacific Biosciences
01-28-2015, 06:29 AM
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Replies: 5
Views: 2,157
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Forum: Sample Prep / Library Generation
12-01-2014, 06:21 AM
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Replies: 2
Views: 3,239
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Forum: Bioinformatics
12-01-2014, 05:48 AM
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Replies: 2
Views: 1,680
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Forum: De novo discovery
11-20-2014, 06:24 AM
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Replies: 8
Views: 3,006
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Forum: Bioinformatics
10-23-2014, 05:47 AM
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Replies: 1
Views: 1,486
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Forum: General
10-06-2014, 12:13 PM
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Replies: 1
Views: 1,048
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Forum: Pacific Biosciences
09-15-2014, 12:41 AM
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Replies: 12
Views: 6,344
Two things you can do:
- rerun quiver (the...
Two things you can do:
- rerun quiver (the final step in the pipeline, RS_Resequencing I believe), this may help
- polish with Illumina data, e.g. 50-100x MiSeq (different tools can do this, e.g....
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Forum: Pacific Biosciences
09-08-2014, 12:41 AM
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Replies: 10
Views: 5,381
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Forum: Bioinformatics
08-07-2014, 05:02 AM
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Replies: 22
Views: 19,764
Hehe, you're right, that is a mistake. The...
Hehe, you're right, that is a mistake. The correct version is
sort -n contig_lengths.txt | awk '{len[i++]=$1;sum+=$1} END {for (j=0;j<i+1;j++) {csum+=len[j]; if (csum>=sum/2) {print...
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