Trimming or filtering the data from Solid

[anusha]

Hi ..

I have got the solid csfatsa file and the data has lot of dots in the sample. So i there any way i can trim or filter the Data in Bowtie,Maq or in another tools that you could suggest.
Here the sample of the data.

>1_17_228_F3
T.1002.312..0..001.0001.2....1..1..022..0....00... 0
>1_17_469_F3
T.1300.333..0..020.1020.0....0..1..020..3....01... 3
>1_17_578_F3
T.1002.321..0..021.0230.0....1..2..122..1....11... 2
>1_17_581_F3
T.1002.322..0..021.0011.0....2..1..021..2....20... 1
>1_112_1012_F3
T.0300.3330.110021010300000000022130200.31.1.01.0. 3
>1_112_1459_F3
T.1002.3201.002000003212002001021200223.10.3.30.2. 3
>1_113_39_F3
T.1000.3330.000001000010100000121000220.10.0.01.0. 0
>1_113_233_F3
T.1001.3211.012000000110102021021120220.00.0.31.2. 0
>1_113_329_F3
T.1300.3330.011220010200000000122130200.01.0.01.0. 3
>1_113_835_F3
T.1300.3330.012220010200002022122230202.01.1.01.2. 3

Thanks
Anu

[nilshomer]

Hi ..

I have got the solid csfatsa file and the data has lot of dots in the sample. So i there any way i can trim or filter the Data in Bowtie,Maq or in another tools that you could suggest.
Here the sample of the data.

>1_17_228_F3
T.1002.312..0..001.0001.2....1..1..022..0....00... 0
>1_17_469_F3
T.1300.333..0..020.1020.0....0..1..020..3....01... 3
>1_17_578_F3
T.1002.321..0..021.0230.0....1..2..122..1....11... 2
>1_17_581_F3
T.1002.322..0..021.0011.0....2..1..021..2....20... 1
>1_112_1012_F3
T.0300.3330.110021010300000000022130200.31.1.01.0. 3
>1_112_1459_F3
T.1002.3201.002000003212002001021200223.10.3.30.2. 3
>1_113_39_F3
T.1000.3330.000001000010100000121000220.10.0.01.0. 0
>1_113_233_F3
T.1001.3211.012000000110102021021120220.00.0.31.2. 0
>1_113_329_F3
T.1300.3330.011220010200000000122130200.01.0.01.0. 3
>1_113_835_F3
T.1300.3330.012220010200002022122230202.01.1.01.2. 3

Thanks
Anu

SOLiD raw data is usually more liberally returned then say Illumina data so you will notice more reads with dots etc. You could use an aligner that can handle the dots (such as BFAST; I am the author of BFAST). I suspect the vast majority of your reads don't have dots. As for primer sequence, programs like BFAST will align those as an insertion at the end of the read.

[hersh]

You can use csfasta quality filter file which is avaliable on solidsoftwaretools under denovo accessory tools.

[av_d]

u can use SOLiD™ Accuracy Enhancement Tool

http://solidsoftwaretools.com/gf/project/saet/

[carmeyeii]

SAET does not only deleting the reads which do not pass the threshold, or trimming the bases which do not either, but it also makes some sort of consensus of reads, which is something you might not want to do if you want to know that what is there is what came out of the machine, as is.

I recommend q-trim from the cartwright lab, it is in python.