csfasta --> fasta conversion - Page 2

inesdesantiago · 10-05-2009, 10:22 AM

Thanks for the reply

I have a collection of reads that are 35 nuc long.
In all of them there is a '.' in the same position, so when I translate from
colorspace to basesapce all of my reads became only 23 nucleotides long plus a tail of 12 N's:

TCGAATGACTGTGACGTGCAGTCNNNNNNNNNNNN

this is happening to all reads in the file. Maybe something went wrong with the sequencing?

For mapping proposes, do you thing that it's better to use the 23nuc reads then the ones with the 'Ns'? I guess if I use the reads with so many N's they can actually map to wrong positions.
Is this right?

Thank you
Ines

inesdesantiago · 10-05-2009, 10:24 AM

Dear westerman,
Thanks for the reply

I have a collection of reads that are 35 nuc long.
In all of them there is a '.' in the same position, so when I translate from
colorspace to basesapce all of my reads became only 23 nucleotides long plus a tail of 12 N's:

TCGAATGACTGTGACGTGCAGTCNNNNNNNNNNNN

this is happening to all reads in the file. Maybe something went wrong with the sequencing?

For mapping proposes, do you thing that it's better to use the 23nuc reads then the ones with the 'Ns'? I guess if I use the reads with so many N's they can actually map to wrong positions.
Is this right?

Thank you
Ines

westerman · 10-05-2009, 10:25 AM

Using the 23nuc reads would be good. Even better is to do your mapping in colorspace without doing translation first. That way sequencer errors should be taken care of.

inesdesantiago · 10-05-2009, 10:28 AM

That's a good idea, I haven't thought about mapping using colorspace...
To bad bowtie doesn't map with colorspace yet..
Regards,
Ines

Chipper · 10-05-2009, 01:31 PM

Quote:

Originally Posted by inesdesantiago

That's a good idea, I haven't thought about mapping using colorspace...
To bad bowtie doesn't map with colorspace yet..
Regards,
Ines

Try bwa (in colorspace) with a seed length of <=22, or better yet a program that allows masking of the position with dots (I think mapreads can do it, maybe others can as well).

westerman · 10-06-2009, 07:02 AM

You can mask using the mapreads via the '-p' parameter. Usually this is done via the matching_large_genomes_cmap_save_script.pl program although other SOLiD routines also call mapreads.

E.g., try '-p 1111111111111111111100000000000000000000' or whatever fits your tag length and desired pattern.

mapreads will still try to map the full length tag and thus will have problems when the masked part seemingly overhangs the ends. That is, mapreads does chop off the masked part to make a shorter read but rather keeps the read full length.

gladexp · 03-08-2012, 05:32 PM

Quote:

Originally Posted by westerman

The ABI 'corona lite' programs (which are free) include 'encodeFasta.py' which will encode and decode to/from color-space, base-space and that abomination 'double-encoded'-space.

Hi all,

Does any one have the link or zipped file for the ABI 'corona lite'?

Many thanks.

idonaldson · 03-09-2012, 03:33 AM

Try this for Corona-Lite, i couldn't seem to find it on Life Techs site:
http://skip.ucsc.edu/phage_contigs/hartzog_phage/tools/

gladexp · 03-09-2012, 06:02 AM

Quote:

Originally Posted by idonaldson

Try this for Corona-Lite, i couldn't seem to find it on Life Techs site:
http://skip.ucsc.edu/phage_contigs/hartzog_phage/tools/

Thanks. I just checked "corona_lite_v4.0r2.0.tgz", is it the latest version?

westerman · 03-12-2012, 09:06 AM

Quote:

Originally Posted by gladexp

Thanks. I just checked "corona_lite_v4.0r2.0.tgz", is it the latest version?

Probably. Corona lite is rather old. We've gone through Bioscope and are now using LifeScope since CL was released.

idonaldson · 03-12-2012, 09:35 AM

I think i used to use 4.2.2. But i don't have the archive to install it (i didn't install it on our cluster).

flashton · 04-04-2012, 01:58 AM

Hi,

I just want to reiterate how crazy double encoding is! Thought we were having problems with our aligner as the 'reads' weren't mapping to the reference. Why on earth did ABI pick those 4 letters? Why even double encode in the first place?!

Thanks Rick!

04-05-2012, 10:27 AM

i hope people realize converting to fastq is probably one of the worst ways to analyze cs data.

flashton · 04-05-2012, 10:38 AM

SeqAA, could you describe your workflow?

colindaven · 04-10-2012, 03:47 AM

SeqAA - agree.

People, if you want to analyse Solid data properly use colour space. If you're forced into the dark arts of base space conversion i.e. for de novo assembly I would strongly recommend reading the supplements of this paper:

Iverson et al. 2012, Science : Untangling genomes from metagenomes ....

vswilliamson · 05-15-2012, 10:27 AM

I generally use galaxy to do most of my conversions

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10-05-2009, 10:22 AM	#21
inesdesantiago Member Location: LONDON, UNITED KINGDOM Join Date: Jan 2009 Posts: 44	Thanks for the reply I have a collection of reads that are 35 nuc long. In all of them there is a '.' in the same position, so when I translate from colorspace to basesapce all of my reads became only 23 nucleotides long plus a tail of 12 N's: TCGAATGACTGTGACGTGCAGTCNNNNNNNNNNNN this is happening to all reads in the file. Maybe something went wrong with the sequencing? For mapping proposes, do you thing that it's better to use the 23nuc reads then the ones with the 'Ns'? I guess if I use the reads with so many N's they can actually map to wrong positions. Is this right? Thank you Ines

10-05-2009, 10:24 AM	#22
inesdesantiago Member Location: LONDON, UNITED KINGDOM Join Date: Jan 2009 Posts: 44	Dear westerman, Thanks for the reply I have a collection of reads that are 35 nuc long. In all of them there is a '.' in the same position, so when I translate from colorspace to basesapce all of my reads became only 23 nucleotides long plus a tail of 12 N's: TCGAATGACTGTGACGTGCAGTCNNNNNNNNNNNN this is happening to all reads in the file. Maybe something went wrong with the sequencing? For mapping proposes, do you thing that it's better to use the 23nuc reads then the ones with the 'Ns'? I guess if I use the reads with so many N's they can actually map to wrong positions. Is this right? Thank you Ines

10-05-2009, 10:25 AM	#23
westerman Rick Westerman Location: Purdue University, Indiana, USA Join Date: Jun 2008 Posts: 1,104	Using the 23nuc reads would be good. Even better is to do your mapping in colorspace without doing translation first. That way sequencer errors should be taken care of.

10-05-2009, 10:28 AM	#24
inesdesantiago Member Location: LONDON, UNITED KINGDOM Join Date: Jan 2009 Posts: 44	That's a good idea, I haven't thought about mapping using colorspace... To bad bowtie doesn't map with colorspace yet.. Regards, Ines

10-06-2009, 07:02 AM	#26
westerman Rick Westerman Location: Purdue University, Indiana, USA Join Date: Jun 2008 Posts: 1,104	You can mask using the mapreads via the '-p' parameter. Usually this is done via the matching_large_genomes_cmap_save_script.pl program although other SOLiD routines also call mapreads. E.g., try '-p 1111111111111111111100000000000000000000' or whatever fits your tag length and desired pattern. mapreads will still try to map the full length tag and thus will have problems when the masked part seemingly overhangs the ends. That is, mapreads does chop off the masked part to make a shorter read but rather keeps the read full length.

03-09-2012, 03:33 AM	#28
idonaldson Member Location: Manchester, UK Join Date: Oct 2009 Posts: 37	Try this for Corona-Lite, i couldn't seem to find it on Life Techs site: http://skip.ucsc.edu/phage_contigs/hartzog_phage/tools/

03-12-2012, 09:35 AM	#31
idonaldson Member Location: Manchester, UK Join Date: Oct 2009 Posts: 37	I think i used to use 4.2.2. But i don't have the archive to install it (i didn't install it on our cluster).

04-04-2012, 01:58 AM	#32
flashton Member Location: london, uk Join Date: Feb 2011 Posts: 10	Hi, I just want to reiterate how crazy double encoding is! Thought we were having problems with our aligner as the 'reads' weren't mapping to the reference. Why on earth did ABI pick those 4 letters? Why even double encode in the first place?! Thanks Rick!

04-05-2012, 10:27 AM	#33
SeqAA Guest Posts: n/a	i hope people realize converting to fastq is probably one of the worst ways to analyze cs data.

04-05-2012, 10:38 AM	#34
flashton Member Location: london, uk Join Date: Feb 2011 Posts: 10	SeqAA, could you describe your workflow?

04-10-2012, 03:47 AM	#35
colindaven Senior Member Location: Germany Join Date: Oct 2008 Posts: 415	SeqAA - agree. People, if you want to analyse Solid data properly use colour space. If you're forced into the dark arts of base space conversion i.e. for de novo assembly I would strongly recommend reading the supplements of this paper: Iverson et al. 2012, Science : Untangling genomes from metagenomes ....

05-15-2012, 10:27 AM	#36
vswilliamson Junior Member Location: Virginia Join Date: Jun 2010 Posts: 2	I generally use galaxy to do most of my conversions