How to process ABI SOLID4 fastq

Question

[Zhixue]

I downloaded a sample of single-end length 50bp RNA-seq with ABI SOLID4 platform from GEO, its fastq file seems like this:
@SAMPLE1.41421928
T20210231231233023100313033020103033311231200111.22
+
!:5967<<9;967;:7;:797759569987*1563$8,6,2)1&.&,,!4%

How can I process these fastq reads so that they can be mapped with normal aligners(STAR/hisat/bwa)?

Answer 1

[h.mon]

It is probably better to use a colorspace aligner, as they accommodate sequencing errors better than if you transform the reads to basespace and then map - due to the nature of solid sequencing, when converting from colorspace to basespace, a sequencing error will propagate down to the end of the read.

I recently used CUSHAW3 with good results. Bowtie (but not Bowtie2) and MOSAIK can also align directly colorspace reads.

[Zhixue]

Thank you very much, I have got the point~