Hi, I'm working 16s rRNA analysis. Recently I got my Illumina sequences for my sample. I have my sequence with 001_R1 AND 001_R2 with 155 dual sample sequence. Do I need to rename the fastq files or I should make some oligo for making stability files

1

Hi, I’m working 16s rRNA analysis. Recently I got my Illumina sequences for my sample. I have my sequence with 001_R1 AND 001_R2 with 155 dual sample sequence. Do I need to rename the fastq files or I should make some oligo for making stability files.
F3D0 F3D0_S188_L001_R1_001.fastq F3D0_S188_L001_R2_001.fastq
F3D141 F3D141_S207_L001_R1_001.fastq F3D141_S207_L001_R2_001.fastq
F3D142 F3D142_S208_L001_R1_001.fastq F3D142_S208_L001_R2_001.fastq
F3D143 F3D143_S209_L001_R1_001.fastq F3D143_S209_L001_R2_001.fastq
F3D144 F3D144_S210_L001_R1_001.fastq F3D144_S210_L001_R2_001.fastq
INSTEAD I could see blank page in the notepad only with the mock.

IMG_20240103_112941
IMG_20240103_1129411920×4221 870 KB

2

Can you try using the make.file function to get mothur to build the file for you?

Pat

3

Hi, Yes I did it, while its coming to make into groups I’m getting struck. Actually I have my FASTQ files looks as follows,
@A00877:943:HMMG3DRXY:2:2101:21187:1047 1:N:0:TAAGGCGA+ATTAGACG
GTGTGTCAGCCGCCGCGGTAATACGAAGGGGGCTAGCGTTGCTCGGAATTACTGGGCGTAAAGCGCACGTAGGCGGCTTTCTAAGTCGGGGGTGAAATCCTGGAGCTCAACTCCAGAACTGCCTTCGATACTGGAAAGCTCGAGTCCGGGAGAGATGAGTGGAACTGCGAGTGTAGAGGTGAAATTCGTAGATATTCGCAAGAACACCAGTGGCGAAGGCGGCTCACTGGCCCGGTACTGACGCTGAGGT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFF:FFFFFFFFF:FFFFFFF,FFFFFFFFF,FFFFFFFFFFFFFFFFFF:FFFFFFFF:FFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFF:F:FF:F:FFFFFF

4

Can you post the names of your fastq files and your files file?

Pat

5

I have some dual fastq files from illumina, where I was not able to upload to the directory for analysis. While I’m trying to upload with mothur SOP (make.file) command. I’m not getting the stability files because my header of each fastq files have the sequence code not the sequence number as follows,
@A00877:943:HMMG3DRXY:2:2101:21187:1047 1:N:0:TAAGGCGA+ATTAGACG
GTGTGTCAGCCGCCGCGGTAATACGAAGGGGGCTAGCGTTGCTCGGAATTACTGGGCGTAAAGCGCACGTAGGCGGCTTTCTAAGTCGGGGGTGAAATCCTGGAGCTCAACTCCAGAACTGCCTTCGATACTGGAAAGCTCGAGTCCGGGAGAGATGAGTGGAACTGCGAGTGTAGAGGTGAAATTCGTAGATATTCGCAAGAACACCAGTGGCGAAGGCGGCTCACTGGCCCGGTACTGACGCTGAGGT

6

Sorry, I’m not following what you’re saying. It would help me to help you if you could post the names of your fastq files and the contents of your files file

Pat