correct bustools commands

README.Rmd

@@ -328,12 +328,22 @@ The `/data/share/MADT/scrnaseq/10xv2_whitelist.txt` contains all the barcodes kn
 We are ready to make the gene count matrix. First, `bustools` runs barcode error correction on the bus file. Then, the corrected bus file is sorted by barcode, UMI, and equivalence classes. Then the UMIs are counted and the counts are collapsed into gene level.
 
 ```{bash bustools, eval=F}
-mkdir—p results/hgmm_1k/genecount tmp
-singularity exec /data/share/MADT/scrnaseq/kallistobustools_0.24.4.simg sh—c "\
-  bustools correct—w data/whitelist_v2.txt -p results/hgmm_1k/output.bus | \
+mkdir -p results/hgmm_1k/genecount tmp
+singularity exec /data/share/MADT/scrnaseq/kallistobustools_0.24.4.simg sh -c "\
+  bustools correct -w data/whitelist_v2.txt -p results/hgmm_1k/output.bus | \
   bustools sort -T tmp/ -t 4 -p - | \
   bustools count -o results/hgmm_1k/genecount/genes -g results/hgmm_1k/tr2g_hgmm.tsv \
-  -e results/hgmm_1k/matrix.ec -t results/hgmm_1k/transcripts.txt --genecounts—"
+  -e results/hgmm_1k/matrix.ec -t results/hgmm_1k/transcripts.txt --genecounts -"
+
+mkdir -p results/hgmm_1k/genecount tmp
+cp /data/share/MADT/scrnaseq/10xv2_whitelist.txt data/whitelist_v2.txt
+cp /data/share/MADT/scrnaseq/hgmm_1k/tr2g_hgmm.tsv data/
+singularity exec /data/share/MADT/scrnaseq/kallistobustools_0.24.4.simg sh -c "\
+  bustools correct -w data/whitelist_v2.txt -p results/hgmm_1k/output.bus | \
+  bustools sort -T tmp/ -t 4 -p - | \
+  bustools count -o results/hgmm_1k/genecount/genes -g data/tr2g_hgmm.tsv \
+  -e results/hgmm_1k/matrix.ec -t results/hgmm_1k/transcripts.txt --genecounts -"
+
 ```
 
 The run logs information is accessible in `json` format in the `results/hmm_1k/` directory.