Changes between Version 39 and Version 40 of SOP/scRNA-seq

Timestamp:

03/23/21 09:59:16 (5 years ago)

Author:

thiruvil

Comment:

--

SOP/scRNA-seq

@@ -41 +41 @@
 write.table(crm.matrix, "My.cellranger.matrix.txt", sep="\t", quote=F)
 }}}
+      * For experiments using hashing or CITE-Seq,
+{{{
+#use CITE-seq-Count (https://hoohm.github.io/CITE-seq-Count)
+CITE-seq-Count -R1 R1_001.fastq.gz -R2 R2_001.fastq.gz -t tags.csv -cbf 1 -cbl 16 -umif 17 -umil 28 -cells 4000 -o CITESeq_Count_Out
+#10X cell barcode is usually first 16 bases
+#cbf, cell barcode first position, 1
+#cbl, cell barcode last position, 16
+
+#umi is usually the next 12 bases (for V3 chemistry), use 10 bases (for V2 chemistry)
+#umif, umi first position, 17
+#umil, umi last position, 28
+
+#FASTQC can be also used to verify if the above positions look correct
+
+#cells, expected number of cells (use Loupe browser to get estimate)
+
+#CITESeq_Count_Out will contain similar output to usual 10X which can be read-in, e.g
+data.htos<-Read10X("CITESeq_Count_Out/umi_count/", gene.column=1)
+}}}
+    Combine/intersect CITE-seq-Count matrix in Seurat using HTODemux in Seurat [[https://satijalab.org/seurat/archive/v3.1/hashing_vignette.html | Demultiplexing with hashtag oligos (HTOs)]]