Originally posted by Brian Bushnell
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1. https://www.ncbi.nlm.nih.gov/books/NBK21729/ (Molecular Cell Biology) summarises:
- "Like pre-mRNAs, the primary transcripts produced from pre-rRNA and tRNA genes undergo extensive processing." - some of the processes are described in the linked chapter. Some things to be aware of if aligning to rRNA...
2. Low quality reads... I have just such reads to back this up... what does Q2 mean here? The reads line up - but the sequence was still read where the quality was #/Q2. To me that looks like a valid read. [Read ID anonymised to SRR888888]
@SRR888888.19.1 19 length=76
CCCCCATGGAGCACAGGCAGACAGAAGCCCCCGCCCCAGCTCTGTGGCCTCAAGCCAGCCTTCCGCTCCTTGAAGC
+
=<7<=<AABCBBABB3?+<A<B>@A###################################################
@SRR888888.20.1 20 length=76
CCCCATGGAGCACAGGCAGACAGAAGTCCCCGCCCCAGCTGTGTGGCCTCAAGCCAGCCTTCCGCTCCTTGAAGCT
+
@@@DDBDDF?BBF?FE=EE1CFDCFHBC<CEFDFA@@F>AGDG@FEHE>EEH>=CCED?CCCC<@@@@CCACCCA@
@SRR888888.29.1 29 length=76
CAGCTGTGTGGCCTCAAGCCAGCCTTCCGCTCCTTGAAGCTGGTCTCCACACAGTGCTGGTTCCGTCACCCCCTCC
+
@@@FFFDE<DFHBAGGEGIHIB@GIIIGIIAHIGIIIGIGHGCHIIIIICFH;FHGGIII@C=?AEHBBCBCCCCC
Oliver
[biologist and programmer ]
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