SEQanswers

Go Back   SEQanswers > Sequencing Technologies/Companies > SOLiD



Similar Threads
Thread Thread Starter Forum Replies Last Post
Updated How to convert .txt file to .bed .GFF or .BAR file format, forevermark4 Bioinformatics 2 06-30-2014 05:02 AM
How to convert SRF file to standard SOLiD output? mart555 Bioinformatics 1 10-19-2012 08:28 AM
Are there any good ways to use SAMtools java API to convert .bam file into .txt file? alextree Bioinformatics 8 01-24-2012 09:20 AM
Counting mapped nucleotides in a bam file moriah Bioinformatics 7 08-22-2011 01:30 AM
Convert Solid BAM/SAM to Solid GFF? ioannis Bioinformatics 0 07-20-2010 07:06 AM

Reply
 
Thread Tools
Old 08-08-2014, 02:35 AM   #1
shunyip
Member
 
Location: New York

Join Date: Oct 2013
Posts: 20
Post Convert 0123 into nucleotides from a SOLiD srf file.

I downloaded some .srf files from GEO, which are RNA-seq data. By using the Staden Package, I was able to do the followings

When I use srf_dump_all, the results look like this:
Code:
[Info]

[Trace]
VAB_ESC_A1.max2302_1929_1121_F3,1.4678048.1.50.38.3###

[Header]
7               # format
0               # NPoints
50              # NBases
0               # NFlows
0               # maxTraceVal
0               # baseline
0               # leftCutoff
51              # rightCutoff

[Bases]
0 00000 +00 +00 +00 +00 #  0
0 00001 +00 +00 +00 +00 #  1
2 00002 +00 +00 +00 +00 #  2
1 00003 +00 +00 +00 +00 #  3
1 00004 +00 +00 +00 +00 #  4
2 00005 +00 +00 +00 +00 #  5
0 00006 +00 +00 +00 +00 #  6
0 00007 +00 +00 +00 +00 #  7
1 00008 +00 +00 +00 +00 #  8
1 00009 +00 +00 +00 +00 #  9
3 00010 +00 +00 +00 +00 # 10
3 00011 +00 +00 +00 +00 # 11
0 00012 +00 +00 +00 +00 # 12
0 00013 +00 +00 +00 +00 # 13
1 00014 +00 +00 +00 +00 # 14
3 00015 +00 +00 +00 +00 # 15
3 00016 +00 +00 +00 +00 # 16
3 00017 +00 +00 +00 +00 # 17
2 00018 +00 +00 +00 +00 # 18

...
I understand that it probably means that there are no quality score, so I gave up on converting it into fastq.

So, I ran it with srf2fasta, and the result looked like this:
Code:
>VAB_ESC_A1.max502_1581_384_F3,1.-4766655.1.46.42.2###
01233303132002231201222021220313221233322222021122
>VAB_ESC_A1.max1676_1611_977_F3,1.4766656.1.46.46.0###
00203223332122313022120222102132200231303332120202
>VAB_ESC_A1.max1901_463_960_F3,1.4766656.1.46.46.0###
00203223332122313022120222102132200231303332120202
>VAB_ESC_A1.max2016_1623_357_F3,1.-4766656.1.46.44.1###
22123330313200223120122202122031322123332232202223
>VAB_ESC_A1.max1843_1702_1379_F3,1.4766657.1.46.46.0###
02032233321223130221202221021322002313033321202020
>VAB_ESC_A1.max1849_392_964_F3,1.4766658.1.44.44.0###
20322333212231302212022210213220023130333212220202
...
Now, I am wondering what do 0,1,2,3 represent.
In other words, does 0 mean A,C,G or T? and also does 1 mean A,C,G or T? and etc

Thank you for your help,
Ken
shunyip is offline   Reply With Quote
Old 08-08-2014, 04:06 AM   #2
mbblack
Senior Member
 
Location: Research Triangle Park, NC

Join Date: Aug 2009
Posts: 245
Default

You need to use abi-dump (see the NCBI documentation for the SRA tools) if you wish to properly convert srf files into color space read (csfasta files) and associated color space quality scores (csqual files).

You want to keep those files in color space if you plan to do anything with them.

Literally, a 0 means a blue color space read, a 1 means a green, a 3 means a yellow and a 4 means a red

see http://seqanswers.com/forums/showthread.php?t=10 for details on ABI color space sequence reads

You can also look at https://www.biostars.org/p/43855/ to explain SOLiD color coding in read files.
__________________
Michael Black, Ph.D.
ScitoVation LLC. RTP, N.C.

Last edited by mbblack; 08-08-2014 at 08:14 AM.
mbblack is offline   Reply With Quote
Reply

Tags
fasta, nucleotides, numbers, solid, srf

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 05:56 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO