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Old 11-18-2013, 03:54 AM   #1
BambooGarden
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Default SHRIMP and indexing

Hello everyone,

I have reads from SOLiD sequencing that were in csfasta + .qual files.
After merging them into csfastq format I would like to align them in colorspace to a reference genome. Does the reference genome have to be indexed for this? and how can I do this?

Also, SHRiMP doesn't seem to be too happy about the csfastq format that I'm providing. I'm getting the following error:

"unrecognized character [0] in input file, try disabling auto-detaction."

I'm already disabling auto-detection by using the -Q command to indicate fastq format.

Any help greatly appreciated.
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Old 09-03-2014, 01:43 AM   #2
Lv Ray
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Have you solved your problem? I don't know how to do the quality control. do you know?
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Old 09-17-2014, 11:42 AM   #3
AntonioRFranco
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I did some quality control in some old SOLiD reads that a colleague of mine had kept for several years

1. First I merged cfasta and qual SOLiD files in a single fastqc file using solid2fastq.c (found in the BFAST package (a search into GitHub makes the miracle of finding the file. You need to compile the C source into a executable or I can send you the executable file if requested)

solid2fastq makes a nice work merging the color spaced data and the quality values into a single fastqc file that you can then analyze with FastQC. FastQC recognizes the color spaced sequence without trouble
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Old 09-17-2014, 10:19 PM   #4
Lv Ray
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Quote:
Originally Posted by AntonioRFranco View Post
I did some quality control in some old SOLiD reads that a colleague of mine had kept for several years

1. First I merged cfasta and qual SOLiD files in a single fastqc file using solid2fastq.c (found in the BFAST package (a search into GitHub makes the miracle of finding the file. You need to compile the C source into a executable or I can send you the executable file if requested)

solid2fastq makes a nice work merging the color spaced data and the quality values into a single fastqc file that you can then analyze with FastQC. FastQC recognizes the color spaced sequence without trouble
Thank you, but I want to try the Bfast, it seems hard but I have got some results.Thank you.
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Old 09-17-2014, 11:05 PM   #5
AntonioRFranco
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BFast facilitates the fast and accurate mapping of short reads to reference sequences, where mapping billions of short reads with variants is of utmost importance

You asked control quality. I answered. Ensure you do it before going beyond
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Old 09-18-2014, 01:30 AM   #6
Lv Ray
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Quote:
Originally Posted by AntonioRFranco View Post
BFast facilitates the fast and accurate mapping of short reads to reference sequences, where mapping billions of short reads with variants is of utmost importance

You asked control quality. I answered. Ensure you do it before going beyond
Thank your for your reminding. My reads is cs-fastq, maybe they can do QC by fastqc directly like you said. I did, it seems that my datasets are not ideal.
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