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Hi,
I have question regarding how detailed my analysis is working. I briefly explain my experiment.
I am depleting an essential helicase from my strain, and I expect to see quite big amount of significantly expressed genes in my data, but there is only 16, which mostly are not relating to the helicase I am depleting.
I am following the protocol by Trapnell et al, with not much changes in options, since I am very new to this field. I use iGenome EF2 for S. pombe as reference and indexes for bowtie.
I tried the option for bowtie2 very-sensitive but not much change had happened. Then I used bowtie1 and it increased the number of genes from 16 to 25.
Another problem is I even can't find some genes when I manually look for them one by one. So it looks that it doesn't map all of the genes. I can say that when I randomly search for genes, it finds genes from all chromosomes I, II and III, but it seems not all genes from all chromosomes are available.
How can I make sure the mapping, indexing and all the steps are working correct? And how can I raise the accuracy of the data analysis so the program can find all the genes?
Your help is deeply appreciated,
Parham
I have question regarding how detailed my analysis is working. I briefly explain my experiment.
I am depleting an essential helicase from my strain, and I expect to see quite big amount of significantly expressed genes in my data, but there is only 16, which mostly are not relating to the helicase I am depleting.
I am following the protocol by Trapnell et al, with not much changes in options, since I am very new to this field. I use iGenome EF2 for S. pombe as reference and indexes for bowtie.
I tried the option for bowtie2 very-sensitive but not much change had happened. Then I used bowtie1 and it increased the number of genes from 16 to 25.
Another problem is I even can't find some genes when I manually look for them one by one. So it looks that it doesn't map all of the genes. I can say that when I randomly search for genes, it finds genes from all chromosomes I, II and III, but it seems not all genes from all chromosomes are available.
How can I make sure the mapping, indexing and all the steps are working correct? And how can I raise the accuracy of the data analysis so the program can find all the genes?
Your help is deeply appreciated,
Parham