Hello! Thank you so much.
"If the reads are in Casava 1.8 paired end demultiplexed format, barcode sequence should be indicated in the files names right after sample ID."
Do you mean the Casava 1.8 format must have the barcode sequence on the file name? If so, I don't think I have this kind of file names. Here is an example of my file names:
210623Helob01_S100_L001_R1_001.fastq.gz
210623Helob01_S100_L001_R2_001.fastq.gz
I notice the example from QIIME 2 (Importing data — QIIME 2 2022.8.3 documentation). There is no barcode sequences on the name of Casava 1.8 fastq.gz file. Can you tell me the if the Casava 1.8 data's barcodes have been removed or not?
Or you mean the barcodes is in the fastq file. I check the head of the F and R reads files
head 210623Helob01_S100_L001_R1_001.fastq
@M01676:287:000000000-JV275:1:1101:15959:1387 1:N:0:ACTACGAC+CTGCGTGT
TACGAGTGCTTCGAGCGTTATCCGGAATCATTGGGCGTAAAGGGTGTGTAGGCGGCGTGGTTAGTCTTCTGTAAAATCCTTGGGCTCAACCGGGGGCTGGCGGTGGAAACGGCAGCGCTTAAGTCCGGGGGAGGTATCTGGATGTCAGGTGGTAGCGGGGAAAGGCGAGGATATCATGGGGAACACCAAAGGCGAAGGCAAGAAACTGGCCCGCTCCTGCCGCTGAGACACGAAAGCGTGGGGAGCGAATG
+
>>AA1>1>1BDFAGBE0AEEGGHGGCAFBGHHCFHGCEGEFFH/BCA/BEFGBEC/>E//?/1BBGF2F2BGFDGHHFG121BGFHHHGFG//<>//A/?/@-<<.<GD/[email protected]:.0:0009;?---9=-///9;:;9///:/;9/-9///[email protected];@BE-9------/;//B/;/A-AB--;AA--/9--;-;-A9A--//;/FB-A-9=-@B/9/-;9--;-;/-B-;A-AB?BB?;--9---@;F
@M01676:287:000000000-JV275:1:1101:15442:1412 1:N:0:ACTACGAC+CTGCGTGT
CACGTAGGGCGCAAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCTCGTAGGCGGACTGTCACGTCTGCTGTGAAAAGCTAGGGCTTAACCCTGGCCTTGCAGTGGATACGGGCAGACTAGAGGTAGGTAGGGGAGAGTGGAATTCCCGGTGTAGCGGTGAAATGCGCAGATATCGGGAGGAACACCGGTGGCGAAGGCGGTTCTCTGGGCCTTACCTGACGCTGAGGAGCGAAAGCGTGGGGAGCGAACA
+
head 210623Helob01_S100_L001_R2_001.fastq
@M01676:287:000000000-JV275:1:1101:15959:1387 2:N:0:ACTACGAC+CTGCGTGT
CCCATTCGCGACCCACGCTTTCGTGTTTCAGCGTCAGGAGCGGGCCAGTCTCTTGCCTTCGCTTTTGGTGTTCCCCATGATATCAACGCATTTCACCGCTACACCATGAGCTCCAGAGACCTCTCCCGTCCTCAAGCGCTGCCGTTTCCTCCGCGAGCCCTCGGTTGAGCCGAAGGATTTTACAGAAGACTAACAACGCCGCCTACACACCCTTTACGCCCAATGATTCCGGATAACGCCCGAAGCACTCG
+
BBBBBFBFA2DBGGGGCGGFGGGGGHFGHHGHGGGGGHGGHGGGGGGFHFHHDGHHHHHHGG>FFHBEEFHGHFFHCGHHHHHHGHHGGGGGHHHHHGGGGGHGHHHGHGBGGHB1?CGHGHHFH0FDFDAGHHGG1.ACCEFFDGHHFFFHGGG@FAAGGGADGDFFBFFD---AFFFFF/BF/9/9F/F/BFFBE>[email protected]>D.BBFFFFFFFFFB.9>DFEF/BBBFFF-A.;9;.----;;-9BFB/.
@M01676:287:000000000-JV275:1:1101:15442:1412 2:N:0:ACTACGAC+CTGCGTGT
CCTGTTCGCTCCCCACGCTTTCGCTCCTCAGCGTCAGGTAAGGCCCAGAGAACCGCCTTCGCCACCGGTGTTCCTCCCGATATCTGCGCATTTCACCGCTACACCGGGAATTCCACTCTCCCCTACCTACCTCTAGTCTGCCCGTATCCACTGCAAGGCCAGGGTTAAGCCCTAGCTTTTCACAGCAGACGTGACAGTCCGCCTACGAGCTCTTTACGCCCAATAATGCCGGACAACGCTTGCGCCCTACG
Do you think "ACTACGAC+CTGCGTGT" is the barcode?
I just need to figure out if the barcodes have been removed or not. My file name per se doesn't have any barcode information.