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Reads q-index nucleotides one per one

Hello,

I am working with fastq file from cDNA. A complete transcriptome was sequenced using Illumina Tech. I want to know the q-index for each read (nucleotide per nucleotide), now I am using ShortRead package (I work with R).

Does anyone know how to do it?

r rna-seq rna-seq
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updated by h.mon h.mon • written by Manuel Mendoza • Manuel Mendoza

By "q-index (nucleotide per nucleotide)" , do you mean the average sequencing quality per base position, as discussed here?

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written by h.mon h.mon

No, I want the value of q-index per base position for each read... Something like that:

Position 01 02 03 04 05 06 ...
Read_1  30 31 32 32 30 ... 
Read_2 30 32 35 34 32 ...
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updated by WouterDeCoster WouterDeCoster • written by Manuel Mendoza • Manuel Mendoza

I added markup to your post for increased readability. You can do this by selecting the text and clicking the 101010 button. When you compose or edit a post that button is in your toolbar, see image below:

101010 Button

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written by WouterDeCoster WouterDeCoster

1 answer

If I understand you question and comment right, it seems you want the Phred quality score from each base. Well, it is already encoded within the fastq file, it is the line after the line containing only a + (most common, sometimes it repeats the line starting at @). Read an introduction here.

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written by h.mon h.mon

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