Reads q-index nucleotides one per one

Question

[Manuel Mendoza]

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?

[h.mon]

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

[Manuel Mendoza]

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 ...

[WouterDeCoster]

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Answer 1

[h.mon]

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.