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Old 12-13-2018, 03:40 AM   #1
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Default Alignment verification IGV

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.
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