Comments (5)
https://github.com/singleron-RD/CeleScope/blob/master/doc/assay/multi_flv_trust4.md#arguments
When running multi_flv_trust4
, the mapfile needs 4 columns.
1st column: Fastq file prefix
2nd column: Fastq file directory path
The full path of the R1 fastq files will be {Fastq file directory path}/{Fastq file prefix}_*_{R1 Fastq file suffix}
. There are several allowed R1 Fastq file suffix
, e.g. R1.fq.gz
, R1.fastq.gz
, etc. You can find all the valid R1 fastq pattern in the log. It seems that the 2nd column should be /mnt/c/users/dipap/Documents/tcr/fastq_files_backup/
, without C231130001_sCT_.fastq.gz
Allowed R1 patterns:
/mnt/c/users/dipap/Documents/tcr/fastq_files_backup/C231130001_sCT_.fastq.gz/C2311300011.fq
/mnt/c/users/dipap/Documents/tcr/fastq_files_backup/C231130001_sCT.fastq.gz/C2311300011.fq.gz
/mnt/c/users/dipap/Documents/tcr/fastq_files_backup/C231130001_sCT.fastq.gz/C2311300011.fastq
/mnt/c/users/dipap/Documents/tcr/fastq_files_backup/C231130001_sCT.fastq.gz/C2311300011.fastq.gz
/mnt/c/users/dipap/Documents/tcr/fastq_files_backup/C231130001_sCT.fastq.gz/C231130001R1.fq
/mnt/c/users/dipap/Documents/tcr/fastq_files_backup/C231130001_sCT_.fastq.gz/C231130001R1.fq.gz
/mnt/c/users/dipap/Documents/tcr/fastq_files_backup/C231130001_sCT_.fastq.gz/C231130001R1.fastq
/mnt/c/users/dipap/Documents/tcr/fastq_files_backup/C231130001_sCT_.fastq.gz/C231130001R1.fastq.gz
/mnt/c/users/dipap/Documents/tcr/fastq_files_backup/C231130001_sCT_.fastq.gz/C231130001R1_001.fq
/mnt/c/users/dipap/Documents/tcr/fastq_files_backup/C231130001_sCT_.fastq.gz/C231130001R1_001.fq.gz
/mnt/c/users/dipap/Documents/tcr/fastq_files_backup/C231130001_sCT_.fastq.gz/C231130001R1_001.fastq
/mnt/c/users/dipap/Documents/tcr/fastq_files_backup/C231130001_sCT_.fastq.gz/C231130001R1_001.fastq.gz
from celescope.
the error seems to have gone away but although multi_flv_trust4 runs without any errors it finishes pretty fast and without producing any output, meaning that something is still wrong. I am sharing below my files in order to pinpoint which file or configuration leads to the quick no output completion of the command.
this is what i get:
(tcr_analysis) diopap@DIO:/mnt/c/users/dipap/Documents/tcr$ multi_flv_trust4 --mapfile ./vdj.mapfile --ref GRCm38 --thread 8 --seqtype TCR --mod shell
2024-06-01 19:36:20,839 - celescope.tools.multi.parse_mapfile - INFO - start...
2024-06-01 19:36:20,924 - celescope.tools.multi.parse_mapfile - INFO - done. time used: 0:00:00.085204
my path to the files is : /mnt/c/users/dipap/Documents/tcr/fastq_files_backup
the name of the fastqs : 'C231130001_sCT_*R1_001.fastq.gz' 'C231130001_sCT_*R2_001.fastq.gz' (this is one sample of 2 paired end read files , to test my code)
my vdj.mapfile with these 4 columns : C231130001 /mnt/c/users/dipap/Documents/tcr/fastq_files_backup/ C231130001 /mnt/c/users/dipap/Documents/tcr//matched_dir
(matched.dir exists in the ./tcr directory)
Thanks in advance for the help
from celescope.
Have you run the scRNA-Seq data? You need the scRNA-Seq cell barcodes to run the flv_trust4 pipeline.
multi_{assay}
only generate the shell scripts in the shell folder, not actually running the pipeline.
from celescope.
Hello, i thought demultiplexing was part of the multi_flv_trust4. We have performed siCircle for 6samples in singleron germany and we have the fastq files.
Yes i see the commands in the shell script but i dont have anything else apart from the fastqs and the html report.
Thank you!!
from celescope.
Hello there! Our problem with @diopapamath is that we only find guidelines for the multi_{assay} that, as you said, creates a plain shell folder. What about the actual pipeline in terms of the script that we need to execute?
from celescope.
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