SHRIMP and indexing

[BambooGarden]

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.

[Lv Ray]

Have you solved your problem? I don't know how to do the quality control. do you know?

[AntonioRFranco]

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

[Lv Ray]

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.

[AntonioRFranco]

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

[Lv Ray]

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.