hi everyone i am having trancripts reads and i want to map reads back to transcriptome . can anybody tell me which mapping tool is good for 454/roche data.
Your last question asked how you should proceed with performing gene expression analysis using 454 reads. I asked you how many reads you have and you messaged me back saying one sample having 152,246 reads and another having 204,564 reads. The simple answer is that your low number of 454 reads does not provide enough sequencing depth to determine expression levels.
I would look for other sources of data or re-sequence your samples at a higher depth with short read sequencers. There is no gold standard for how many reads you need to cover the transcriptome in sufficient depth for expression analysis since every organism is different, but I would go for at least 10 million reads.
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Have you tried just using tophat/bowtie? That supports colorspace reads (just use bowtie1, not bowtie2).
yes i tried, i did it with bowtie then tophat pipeline but i found lots of unmapped reads and a bad junction file was created . why it is so? you do know that?
Hard to say without seeing the actual data. Given what Damian mentioned in his answer, it sounds like your dataset is too small to be of much use to begin with.