Entering edit mode
3.7 years ago
damt0320
•
0
Hi, im trying to demultiplex a fastq file with demuxbyname.sh. Im using the following code:
demuxbyname.sh in=1-1_S1_L001_R1_001.fastq in2=1-1_S1_L001_R2_001.fastq out=out_%_R1.fq out2=out_%_R2.fq names=pool1.txt substringmode=t delimiter=:
My samples are dual index (barcode in forward and barcode in reverse file). So in the txt file i have the 2 barcodes per ID in the first line (something like ACTCCCG+GTCGGG) and the other ones below like in a column. The fastq files are like the following:
@M03485:29:000000000-J4R9F:1:1101:16497:1353 1:N:0:NCCGGAGA+TATAGCCT
GCCACTAGATCCAAGAGATCCGNTGTTGNAAGTTGTATTTCCAAAATAACCCAAATAATACATTCCATTTAAGAGTTTATAAATAAAATGAAGATCAAGGGGACAATAATAAAAAAGAAAGAGAATACACTCTTCCCTCTTAAACCCTTCTTGACTTCACAAAGTTCACAGGTGTGTAAAGGATGAAAAGTTAATTA$
+
3AA33FCFBFFFFGGGGAGGGG#BBFFG#B2AFFHHHHFFHFBHHGFHHHEEFHHHHHHFFHEGGHFGHHHHHHF5FGHHHHHGHGHDF3@FHFGFHHBGGCEEGHHHHHHHFFFE?FHHHHHHHHFBGHHHHHGGCHCCFFHHGHGGHHGHFHFFHHHFHGCFFFGHHHHHFFDDGHFBFHFGHHHGHHDFHFGFG$
@M03485:29:000000000-J4R9F:1:1101:16985:1388 1:N:0:NCCGGAGA+TATAGCCT
ACTGACTGATGCAAGAGATCCGNTGTTGNAAGTGAACCTTGTTACGACTTTTACTTCCGTATAGTAAGTAGATCGGAAGAGCACACGGCTGAACTCCAGTCACTCCGTAGAATCTCGGATGCCGTCTTCTGCTTGAAAAAAATCAAATATTATGCTTCGCAGATTTCAAACCCGGACCCTTTGTTACGACTTTTCCT$
The program dont show any error, i just dont get any output from the process
Set INTERLEAVED to false
Input is being processed as paired
Time: 3.899 seconds.
Reads Processed: 6470118 1659.47k reads/sec
Bases Processed: 1623999618 416.53m bases/sec
Reads Out: 0
Bases Out: 0
IN another post, the issue was fixed with substringmode=t but not in this case. Any help is appreciated.
Can you run the code I have in this post to make sure you get a list of all indexes that are in your file: C: Demultiplexing reads with index present in the labels
You may need to rev-comp indexes you are searching with and you would get that idea once you see what is there.
You could also try
deML(A: Demultiplexing Illumina data ) as an alternative.