Hey guys, I'm pretty new to the programming and bioinformatics so please bare with me.
Ok, so I'm interested in looking at Differential Gene expression between two US rice cultivars. We used one lane per cultivar in an Illumina sequencer (GA-IIx). For each lane I have about 40 different fastq files. I concatenated all on the individual fastq files into one giant file for each cultivar. I then downloaded the rice genome from MSU and formatted this using 2bwt-builder. Then I did an alignment of the giant fastq file for each cultivar. Once the alignment ran, I used the soap2sam.pl from the soap website to convert the file to sam.
Now that I have the alignments in sam format I'm kind of lost. I need to assign gene annotations to my alignments. I think I need to trim out my low quality matches and then use the gff3 to annotate but I don't know how to go about doing that.
Any advise would be greatly appreciated. If you have suggestions for better alignment software I'd be willing to go that route. I tried using the tuxedo software sweet but kept getting lots of errors so I'd prefer to stay away from that.
Ok, so I'm interested in looking at Differential Gene expression between two US rice cultivars. We used one lane per cultivar in an Illumina sequencer (GA-IIx). For each lane I have about 40 different fastq files. I concatenated all on the individual fastq files into one giant file for each cultivar. I then downloaded the rice genome from MSU and formatted this using 2bwt-builder. Then I did an alignment of the giant fastq file for each cultivar. Once the alignment ran, I used the soap2sam.pl from the soap website to convert the file to sam.
Now that I have the alignments in sam format I'm kind of lost. I need to assign gene annotations to my alignments. I think I need to trim out my low quality matches and then use the gff3 to annotate but I don't know how to go about doing that.
Any advise would be greatly appreciated. If you have suggestions for better alignment software I'd be willing to go that route. I tried using the tuxedo software sweet but kept getting lots of errors so I'd prefer to stay away from that.