Hello folks,
Fairly new to RNA-Seq so here are some quality control questions I've come across and cannot seem to find a good answer to.
After I quality control check my samples with FastQC and proceed with Hisat and samtools, I then check the alignments made using IGV.
However, I've noticed that some of the genes are out by roughly 10-30bp from the reference genome (human 38). Is that ok?
Secondly, if reads map to very few bps for a gene is that gene still a credible hit?
And lastly, is there any concern about having identical mappings of individual genes between different samples?
Thank you.
Fairly new to RNA-Seq so here are some quality control questions I've come across and cannot seem to find a good answer to.
After I quality control check my samples with FastQC and proceed with Hisat and samtools, I then check the alignments made using IGV.
However, I've noticed that some of the genes are out by roughly 10-30bp from the reference genome (human 38). Is that ok?
Secondly, if reads map to very few bps for a gene is that gene still a credible hit?
And lastly, is there any concern about having identical mappings of individual genes between different samples?
Thank you.
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