Forum: Bioinformatics
12-11-2013, 04:56 PM
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Replies: 9
Views: 6,536
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Forum: Bioinformatics
12-11-2013, 01:21 AM
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Replies: 9
Views: 6,536
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Forum: Pacific Biosciences
12-05-2013, 12:21 AM
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Replies: 1
Views: 3,466
Hi,
The options given for Novoalign are not...
Hi,
The options given for Novoalign are not ideal.
If you are using Novoalign with LSC you need to use -r Exhaustive not -r All. This will improve results dramatically and should be better than...
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Forum: Bioinformatics
12-05-2013, 12:18 AM
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Replies: 9
Views: 6,536
Hi Hans,
The options given for Novoalign are...
Hi Hans,
The options given for Novoalign are all wrong.
If you are using Novoalign with LSC you need to use -r Exhaustive not -r All. This will improve results dramatically and should be better...
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Forum: Pacific Biosciences
12-02-2013, 05:26 AM
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Replies: 55
Views: 25,104
Hi,
If you are using Novoalign with LSC you...
Hi,
If you are using Novoalign with LSC you need to use -r Exhaustive not -r All.
From my tests good options are..
novoalign -c1 -r Ex 1000 -t 250 -F FA -g 0 -x 30 -o sam
This will give...
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Forum: RNA Sequencing
10-31-2013, 10:48 PM
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Replies: 2
Views: 2,775
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Forum: Bioinformatics
10-31-2013, 10:40 PM
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Replies: 1
Views: 2,090
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Forum: Bioinformatics
10-31-2013, 10:38 PM
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Replies: 1
Views: 1,510
Hi,
You do not need to specify the qual...
Hi,
You do not need to specify the qual files on the command line, just the csfasta files. NovoalignCS will look for the qual files based on naming convention and use if found.
Colin
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Forum: General
10-31-2013, 10:36 PM
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Replies: 31
Views: 15,634
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Forum: Bioinformatics
10-25-2013, 02:30 AM
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Replies: 514
Views: 223,997
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Forum: Bioinformatics
10-24-2013, 05:33 PM
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Replies: 514
Views: 223,997
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Forum: Bioinformatics
09-30-2013, 01:48 AM
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Replies: 2
Views: 2,184
BAM Extract
Could you send be a extract (samtools view) from the bam file for the region you displayed and I'll take a look at it. Email to support at novocraft-dot-com.
Colin
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Forum: Bioinformatics
09-30-2013, 01:33 AM
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Replies: 2
Views: 2,184
Softclipping
Hi,
I've been back through the change logs and can't find any record of fixing a bug that might cause this. Large amounts of soft clipping like this could be caused by low base qualities...
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Forum: Bioinformatics
07-05-2012, 09:28 PM
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Replies: 0
Views: 1,399
Novosort
Hi,
If you like to try Novosort the download at www.novocraft.com contains a trial license good until 1 September. The latest version includes Name sorting and for coordinate sorting the ability...
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Forum: Bioinformatics
07-05-2012, 09:08 PM
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Replies: 42
Views: 12,588
Intil Xeon Phi
I think there's some hyperthreading so it will be interesting to see.The coprocessor runs Linux and has MPI so hopefully all we need to change in Novoalign is the SSE routines so it should be an easy...
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Forum: Bioinformatics
12-13-2011, 05:56 PM
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Replies: 89
Views: 68,348
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Forum: Bioinformatics
11-22-2011, 05:40 PM
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Replies: 18
Views: 5,299
Hi Justin,
You can do multiple paired end...
Hi Justin,
You can do multiple paired end files using named pipes
mkfifo read1_pipe read2_pipe
cat lane1_read1.fastq lane2_read1.fastq lane3_read1.fastq > read1.pipe
cat lane1_read2.fastq...
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Forum: Bioinformatics
11-21-2011, 09:03 PM
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Replies: 18
Views: 5,299
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Forum: Bioinformatics
11-09-2011, 10:14 PM
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Replies: 94
Views: 161,377
For sure, we believe it's still the best :)
...
For sure, we believe it's still the best :)
Colin
PS. Some mapper comparisons have shown different results but this can be the result of targeting the simulation at the mapper the developer is...
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Forum: Bioinformatics
11-09-2011, 05:22 PM
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Replies: 94
Views: 161,377
That's a ridiculous statement! Most hashed...
That's a ridiculous statement! Most hashed aligners using a 15-mer hash would need 3 equally spaced mismatches in a 50mer to miss an alignment. But there are some hashed based aligners that are can...
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Forum: Bioinformatics
10-04-2011, 07:18 AM
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Replies: 5
Views: 2,633
As you used -i 200 30 the range of fragment...
As you used -i 200 30 the range of fragment length for proper pairs would be 0 to 480. It should be OK as penalties will adjust to the actual distribution. However a few long fragments may not have...
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Forum: Bioinformatics
10-04-2011, 06:57 AM
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Replies: 5
Views: 2,633
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Forum: Bioinformatics
10-03-2011, 06:34 PM
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Replies: 1
Views: 2,276
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Forum: Bioinformatics
10-03-2011, 06:28 PM
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Replies: 2
Views: 1,819
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Forum: Bioinformatics
10-03-2011, 06:20 PM
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Replies: 4
Views: 2,094
Hi,
Novoalign and Stampy both expect reads...
Hi,
Novoalign and Stampy both expect reads of a pair to be orientated so that one reads is on +ve strand, the other on -ve strand with 3' ends of reads towards the centre.
5---------------->3 ...
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