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Forum: Bioinformatics 08-11-2016, 05:46 AM
Replies: 4
Views: 1,097
Posted By flxlex
Nice, @GenoMax, I didn't know about that. Now if...

Nice, @GenoMax, I didn't know about that. Now if only ENA would add that link...
Forum: Bioinformatics 08-04-2016, 05:09 AM
Replies: 4
Views: 1,097
Posted By flxlex
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...
Forum: Bioinformatics 05-05-2016, 01:56 AM
Replies: 6
Views: 754
Posted By flxlex
Newbler 3 will take longer reads, but I can't...

Newbler 3 will take longer reads, but I can't remember the limit, either 20kb, 30kb or 40kb. You could also try the Canu assembler, or FALCON.
Forum: Bioinformatics 11-17-2015, 11:37 PM
Replies: 4
Views: 1,059
Posted By flxlex
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.
Forum: Bioinformatics 11-06-2015, 12:23 PM
Replies: 1
Views: 436
Posted By flxlex
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
Forum: Bioinformatics 10-16-2015, 05:38 AM
Replies: 4
Views: 1,769
Posted By flxlex
Try Pilon from the Broad:...

Try Pilon from the Broad: http://www.broadinstitute.org/software/pilon/
Forum: Bioinformatics 09-28-2015, 07:37 AM
Replies: 12
Views: 1,331
Posted By flxlex
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...
Forum: 454 Pyrosequencing 09-16-2015, 05:55 AM
Replies: 3
Views: 1,949
Posted By flxlex
A problem for what? Depends on your further...

A problem for what? Depends on your further analysis steps, I guess?
Forum: 454 Pyrosequencing 09-15-2015, 05:03 AM
Replies: 3
Views: 1,949
Posted By flxlex
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....
Forum: 454 Pyrosequencing 08-04-2015, 02:40 AM
Replies: 3
Views: 1,919
Posted By flxlex
What is the total coverage (total sequenced bp...

What is the total coverage (total sequenced bp divided by genome size)? Your data should be OK for newbler in one go...
Forum: 454 Pyrosequencing 07-02-2015, 04:50 AM
Replies: 3
Views: 1,919
Posted By flxlex
Not directly out of the box. Do you need all that...

Not directly out of the box. Do you need all that data (what are you assembling)? If you do, can you do digital normalisation, or partioning (e.g., see the khmer (khmer.readthedocs.org) package)
Forum: Bioinformatics 05-13-2015, 06:22 AM
Replies: 1
Views: 680
Posted By flxlex
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...
Forum: Bioinformatics 05-07-2015, 11:45 PM
Replies: 9
Views: 2,353
Posted By flxlex
(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...
Forum: Bioinformatics 02-25-2015, 07:12 AM
Replies: 3
Views: 738
Posted By flxlex
It probably doesn't. Split the 454 paired reads...

It probably doesn't. Split the 454 paired reads using sfftools from Roche, or sff_extract (see methods section of...
Forum: De novo discovery 02-18-2015, 07:00 AM
Replies: 4
Views: 2,848
Posted By flxlex
PacBio recommends 10x coverage in long reads for...

PacBio recommends 10x coverage in long reads for assembly improvement.
Forum: Pacific Biosciences 02-16-2015, 02:53 AM
Replies: 4
Views: 2,317
Posted By flxlex
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...
Forum: Pacific Biosciences 01-28-2015, 06:29 AM
Replies: 5
Views: 1,349
Posted By flxlex
When you choose HGAP, it uses Celera for the...

When you choose HGAP, it uses Celera for the error-correction (and assembly).
Forum: Sample Prep / Library Generation 12-01-2014, 06:21 AM
Replies: 2
Views: 2,419
Posted By flxlex
Follow up information from Illumina: ...

Follow up information from Illumina:



We lost 300 samples and 2 weeks of HiSeq run time...
Forum: Bioinformatics 12-01-2014, 05:48 AM
Replies: 2
Views: 1,112
Posted By flxlex
PacBioToCa has afaik been superseded by PBcR. You...

PacBioToCa has afaik been superseded by PBcR. You can either use the smrtanalysis, or wgs-assembler (aka Celera Assembler) installation for this.

PBJelly does not seem to depend on smrtanalysis...
Forum: De novo discovery 11-20-2014, 06:24 AM
Replies: 8
Views: 2,079
Posted By flxlex
Yes, Newbler will figure out the pairing from the...

Yes, Newbler will figure out the pairing from the fastq files, provided the read IDs conform to the 'standards' (see the fastq entry on wikipedia). No, you cannot tell Newbler the span, as it figures...
Forum: Bioinformatics 10-23-2014, 05:47 AM
Replies: 1
Views: 912
Posted By flxlex
Yep, this is not good - even though the meaning...

Yep, this is not good - even though the meaning of these egde metrics is poorly documented. I would do a bunch of QCs on the reads (not just fastqc, also preqc from SGA) and assembly (concoct for...
Forum: General 10-06-2014, 12:13 PM
Replies: 1
Views: 611
Posted By flxlex
Have a look at pilon:...

Have a look at pilon: http://www.broadinstitute.org/software/pilon/
Forum: Pacific Biosciences 09-15-2014, 12:41 AM
Replies: 12
Views: 4,563
Posted By flxlex
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....
Forum: Pacific Biosciences 09-08-2014, 12:41 AM
Replies: 10
Views: 2,971
Posted By flxlex
And, the read names will tell you which reads are...

And, the read names will tell you which reads are subreads of the same ZMW ('well'). See https://github.com/PacificBiosciences/cDNA_primer/wiki/Understanding-PacBio-transcriptome-data#readexplained,...
Forum: Bioinformatics 08-07-2014, 05:02 AM
Replies: 22
Views: 12,669
Posted By flxlex
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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