yingstat / aligner Goto Github PK

(i)STAR
*Requires: Drop-seq_tools-1.13, picard, samtools, STAR
see dropseq-star.txt

(ii)Kallisto
*Requires: Drop-seq_tools-1.13, picard, samtools, Kallisto
see dropseq-kallisto.txt

(i) STAR
*Requires: fastq, cutadapt, trimalore, STAR, subread
1.obtain the demultiplexed fastqs, see fluidigm_trim.txt
2.see fluidigm_star.txt

(ii) Kallisto
*Requires: fastqc, cutadapt, trimaglore, STAR, subread
1.obtain the demultiplexed fastqs, see fluidigm_trim.txt
2.see fluidigm_kallisto.txt

(iii)
Combine individual feature count output, and reformat to count matrix
awk '{print FILENAME"\t"$0}' *.txt |grep -v Geneid > /tmp.txt
For STAR: see transform.r
For Kallisto: see transform_kallisto.r

(i) STAR
*Requires: STAR 2.7.3
see starsolo10x.txt
(ii) Kallisto with cDNA index
see kbus10x.txt
see Generate_matrix.py
(iii) Kallisto with cDNA+intron index
*Requires: kallisto bustool 0.39.3
see kpbmc.txt
see kbus393.py

(i) STAR
*Requires: STAR 2.7.3
see starcortex1.txt
(ii) Kallisto
*Requires: kallisto bustool 0.39.3
see kcortex1.txt
see kbus393.py

(i) Figure 1, 2
see aligners.R
(ii) Figure 3,4
see pbmc.R
see singlenuclei.R
(iii) Figure 5
see time.py