I am learning the tutorial of Pre-processing of Single-Cell RNA Data
the UMI-tools extract on the tutorial is Galaxy version 0.5.5.1 but the current version is Galaxy Version 1.1.6+galaxy0. The following parameters are not presented on the current version of UMI-tools extract:
“Barcode on both reads?”: Barcode on first read only
“Use Known Barcodes?”: Yes
“Barcode File”*: celseq_barcodes.192.tabular (Input dataset)
“Barcode pattern for first read”: NNNNNNCCCCCC
“Enable quality filter?”: No
I put the following information on UMI-tools extract (Galaxy Version 1.1.6+galaxy0): Library type Paired-end Dataset Collection
Reads in FASTQ format * 7: C57_P1_B1
Barcode pattern for first read * NNNNNNCCCCCC Barcode Extraction Method String
Allowlist of accepted barcodes - optional: 9: celseq_barcodes.192.tabular Enable quality filter? No
This returns 0 bytes in both forward and reverse reads
Would you help me to solve this problem?
Hopefully you discovered this already, but you can navigate the tool versions on the tool form! See → FAQ: Changing the tool version
Sometimes a tutorial uses an older tool version to better match a particular tutorial dataset or teaching method. This is great for learning purposes. Later on you can explore the newer versions with the expanded or modified parameter sets.
Hope you solved this already, or that this helps, or that it helps others who may run into this problem later on!
Sorry for the late reply as I was on holiday. I found a way to solve the problem. First change file type from SAM to tabular, then the 12th (opt) column will be divided to 3 columns. I use the Cut columns from a table tool to cut and choose the column with miRNA name in the format such as XQ:Z:hsa-miR-200b-3p, followed using the Regex Replace tool and set the following parameters: Search String – optional: XQ:Z: Replace String – optional: leave blank. This will give me the miRNA names.
