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Search: Posts Made By: sparks
Forum: Bioinformatics 12-11-2013, 03:56 PM
Replies: 9
Views: 4,412
Posted By sparks
I think you could split the PacBio files with a...

I think you could split the PacBio files with a short perl script. Try and keep subreads together. You then run LSC on each set of PacBio reads and later combine the corrected reads.
Forum: Bioinformatics 12-11-2013, 12:21 AM
Replies: 9
Views: 4,412
Posted By sparks
Use Novoalign or split your PacBio reads into...

Use Novoalign or split your PacBio reads into multiple indexes.
Forum: Pacific Biosciences 12-04-2013, 11:21 PM
Replies: 1
Views: 2,892
Posted By sparks
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...
Forum: Bioinformatics 12-04-2013, 11:18 PM
Replies: 9
Views: 4,412
Posted By sparks
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...
Forum: Pacific Biosciences 12-02-2013, 04:26 AM
Replies: 55
Views: 19,024
Posted By sparks
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...
Forum: RNA Sequencing 10-31-2013, 09:48 PM
Replies: 2
Views: 1,938
Posted By sparks
This works... awk '$14 ~...

This works...

awk '$14 ~ /\+([AGTC][ACGT])/ { print $0}'
Forum: Bioinformatics 10-31-2013, 09:40 PM
Replies: 1
Views: 1,675
Posted By sparks
This should be fixed in later releases.

This should be fixed in later releases.
Forum: Bioinformatics 10-31-2013, 09:38 PM
Replies: 1
Views: 1,136
Posted By sparks
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
Forum: General 10-31-2013, 09:36 PM
Replies: 31
Views: 13,029
Posted By sparks
Hi, Novoalign Version 3 supports reads up to...

Hi,

Novoalign Version 3 supports reads up to 1000bp

Colin
Forum: Bioinformatics 10-25-2013, 01:30 AM
Replies: 513
Views: 184,530
Posted By sparks
Agree you can merge Bowtie and calculate a vague...

Agree you can merge Bowtie and calculate a vague alignment quality. Perhaps you can give Angie the formulae for it.
Forum: Bioinformatics 10-24-2013, 04:33 PM
Replies: 513
Views: 184,530
Posted By sparks
Reply to thread 'Bowtie, an ultrafast, memory-efficient, open source short read align

Hi Angie,

I think if you use split reference you'll have issues calculating the alignment quality of the best alignment during the merge, it's a bit more complicated than just selecting the best...
Forum: Bioinformatics 09-30-2013, 12:48 AM
Replies: 2
Views: 1,761
Posted By sparks
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
Forum: Bioinformatics 09-30-2013, 12:33 AM
Replies: 2
Views: 1,761
Posted By sparks
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...
Forum: Bioinformatics 07-05-2012, 08:28 PM
Replies: 0
Views: 1,086
Posted By sparks
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...
Forum: Bioinformatics 07-05-2012, 08:08 PM
Replies: 42
Views: 10,510
Posted By sparks
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...
Forum: Bioinformatics 12-13-2011, 04:56 PM
Replies: 89
Views: 53,763
Posted By sparks
Hi Gabriele, I never found out about the...

Hi Gabriele,
I never found out about the control bits. The is_filtered is a flag that Illumina sets if they think the read might be from a polyclonal cluster.
Colin
Forum: Bioinformatics 11-22-2011, 04:40 PM
Replies: 18
Views: 4,222
Posted By sparks
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...
Forum: Bioinformatics 11-21-2011, 08:03 PM
Replies: 18
Views: 4,222
Posted By sparks
That's a neat way and it may improve performance...

That's a neat way and it may improve performance as decompression is in its own thread.
One issue with Novoalign is that it reads a few records to check the file format then rewinds the files and...
Forum: Bioinformatics 11-09-2011, 09:14 PM
Replies: 94
Views: 138,423
Posted By sparks
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...
Forum: Bioinformatics 11-09-2011, 04:22 PM
Replies: 94
Views: 138,423
Posted By sparks
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...
Forum: Bioinformatics 10-04-2011, 06:18 AM
Replies: 5
Views: 2,028
Posted By sparks
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...
Forum: Bioinformatics 10-04-2011, 05:57 AM
Replies: 5
Views: 2,028
Posted By sparks
Hi Jane, The insert size will be reported...

Hi Jane,

The insert size will be reported near the end of the log file, SOTON0003a_mapping.stats

Colin
Forum: Bioinformatics 10-03-2011, 05:34 PM
Replies: 1
Views: 1,883
Posted By sparks
http://www.novocraft.com/wiki/tiki-index.php?page=...

http://www.novocraft.com/wiki/tiki-index.php?page=mRNA+and+the+Spliceosome&structure=Novocraft+Technologies&page_ref_id=35
Forum: Bioinformatics 10-03-2011, 05:28 PM
Replies: 2
Views: 1,451
Posted By sparks
The F & R give the direction of the alignment....

The F & R give the direction of the alignment. This will correspond to strand if you have used a strand specific protocol to prepare your sample.
Colin
Forum: Bioinformatics 10-03-2011, 05:20 PM
Replies: 4
Views: 1,688
Posted By sparks
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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