STOmics SAW analysis process supports Q40 FASTQ and Q4 FASTQ files as input parameters.
## Q40 read 1 @V350156489L4C001R00100001484/1 TCTGCAGCCAACATGGACAGATCCTTTTAGAACTT + D>DC<CBEADEABCB(AADCDD2DD"DBE*$F'C' ## Q40 read 2 @V350156489L4C001R00100001484/2 CTATGAAACACACTATCCTCAATCGGCTCCTTAATTTCAATACCAGCCGT + ECFCCB?CAECEBDBCCFDFEFDF?<FCF>B?2EC=C?C<CE(AA=;B5B
## Q4 read @FP300000513L1C002R00400000218 CE242DF29A57 97D26 GTGTAGTGAACCCCATGGTAGTTTTCTGATTGTTGTTAAAAAAAATGACTTAACATATTACATGGACACTCAATAAAAATGTTTTATTTCCTGTTGAAAA + FFFFFFFFFFFF8F8FFFFFFFFFFFFF8FFFFFFFFF8FF8FFF8FFFFFFF,FFFFFFFFFFF8FFFFFF8F8F,F8FFFFFF,FFFFFFFFFF,FFF
--sjdOverhangused for STAR builds of reference genome indexes need to be consistent with the sequencing read length? If there are variable sequencing read lengths, e.g. 50bp, 100bp, 150bp, will SAW choose different STAR indices automatically during analysis?
|0.8X beads (after cDNA release from the tissue)|
The high ratio of beads allows binding of cDNA molecules as many as possible, while leaving impurities from the tissue sample in the supernatant.
|0.6X beads (after cDNA amplification by PCR)|
The beads bind cDNA molecules. Primers and other small DNA fragments will remain in the supernatant and get discarded.
|0.55X beads and 0.15 μL beads (after cDNA fragmentation & amplification)|
Double selection which removes both larger and smaller fragmented DNA and harvests the intermediate fragments.
Original transcription matrix of whole chip area, containing only bin1 geneExp group.
Transcription matrix of tissue-covered region, containing only bin1 geneExp group.
Visual transcription matrix of whole chip area, containing multiple bin geneExp and wholeExp groups.
Cell-gene expression matrix of tissue-covered region.
Completion matrix based on matrix that is extracted by mask of IF image gray scale threshold filtering. [Recommended to name like this, it is not generated by default. Please complete it by running cellCut after tissueCut.]
Cell-gene expression matrix that is extracted by cellmask of IF image gray scale threshold filtering. [Recommended to name like this, it is not generated by default but needed to switch to cellCut after tissueCut.]
Original transcription matrix of labeled area, containing only bin1 geneExp group.
Visual matrix of labeled area, containing multiple bin geneExp and wholeExp groups.
Cell-gene expression matrix of labeled area.