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Old 04-21-2011, 11:37 AM   #1
NanYu
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Default pre-filtering before mapping?

Hi,
We have some mated paired end sequences (50bp) to be mapped to the reference genome for SNP (and maybe indel) discovery.
The data I have are csfasta and qual files.
Could any one let me know if I need to do pre-filtering for the sequences before I use any software to map them?
If I use bowtie, I should remove the orphan reads (and maybe try to map the orphan reads using a different parameter set).
If I use BFAST, should I do the same?

If I do need to filter the sequences based on the quality score, what's the cut-off threshold people normally use? Average of Q10?
How to translate the quality score to the % error rate like the Phred score?

Thanks!
Nan
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Old 04-26-2011, 08:08 PM   #2
fanyucai1
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csfasta_quality_filter.pl this script will be used about qulity contorl in solid.
you can find this script by google
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Old 04-27-2011, 07:24 AM   #3
fenciso
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Hi,

I am on index step, but apparently there is an error:

In function "RGIndexLayoutCreate": Fatal Error[OutOfRange]. Message: Layout must begin with a one.

Could someone help me with this problem???
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Old 04-27-2011, 01:12 PM   #4
NanYu
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Quote:
Originally Posted by fenciso View Post
Hi,

I am on index step, but apparently there is an error:

In function "RGIndexLayoutCreate": Fatal Error[OutOfRange]. Message: Layout must begin with a one.

Could someone help me with this problem???

you mean the indexing of the reference genome using bowtie?

Below is the command I use (assuming bowtie-build and all_reference.fa are in the same folder)

./bowtie-build -C -f all_reference.fa reference_Color
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Old 04-27-2011, 01:16 PM   #5
NanYu
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Quote:
Originally Posted by fanyucai1 View Post
csfasta_quality_filter.pl this script will be used about qulity contorl in solid.
you can find this script by google
Thanks!
I downloaded the program. It has many parameters to use for trimming. Can anyone tell me normally what value they use for filtering (if any)? Thanks!

1. num_colors_to_hard_trim
2. min_median_qv
3. max_bad_colors_in_first_ten
4. max_number_bad_colors
5. num_consec_colors_to_trim
6. trim_terminal_bad_colors
7. min_read_length
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Old 04-27-2011, 05:23 PM   #6
fanyucai1
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solid not supply the parameters, choose them by yourself, i advice you can statistics raw data before using last script.
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Old 04-28-2011, 10:09 AM   #7
NanYu
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Quote:
Originally Posted by fanyucai1 View Post
solid not supply the parameters, choose them by yourself, i advice you can statistics raw data before using last script.
Thanks! I am new in the area and would like some advice on choosing the values for those parameters, such as: Minimum QV value for a single color.

As to the statistics, besides median/average quality score, what else should I look into?

Thanks!
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Old 05-02-2011, 07:59 PM   #8
fanyucai1
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there is a paper called :Analysis of quality raw data of second generation sequencers with Quality Assessment Software. you can find it by google. it is very simple ,it wil help you .
some parameters contains: min \max\Q20\mean\median you should consider
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Old 03-28-2012, 11:01 PM   #9
paolo.kunder
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I downloaded and executet csfasta_quality_filter.pl script on my SOLiD 5500 csfasta (and qual) data to trim a fixed number of colors. ( code below)

perl csfasta_quality_filter.pl -f F5.cs fasta -q F5.QV.qual -o 5_bases_trimmed_F5.csfasta --num_colors_to_hard_trim 5

I was wondering about the output file, from the manual (Filtered and trimmed reads are output in csfasta format to a user-specified filename). And where is my associated QV.qual file trimmed? Any ideas? I cannot supply TopHat or any other alignment software with a trimmed csfasta and a full lenght associated quality file..
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Old 03-29-2012, 02:29 AM   #10
fanyucai1
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Quote:
Originally Posted by paolo.kunder View Post
I downloaded and executet csfasta_quality_filter.pl script on my SOLiD 5500 csfasta (and qual) data to trim a fixed number of colors. ( code below)

perl csfasta_quality_filter.pl -f F5.cs fasta -q F5.QV.qual -o 5_bases_trimmed_F5.csfasta --num_colors_to_hard_trim 5

I was wondering about the output file, from the manual (Filtered and trimmed reads are output in csfasta format to a user-specified filename). And where is my associated QV.qual file trimmed? Any ideas? I cannot supply TopHat or any other alignment software with a trimmed csfasta and a full lenght associated quality file..
This script could not output the .qual file after quality-contorl ,you could choose it from raw file according csfasta file .
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