Originally posted by simonandrews
View Post
A couple of notes:
In the help it lists the option flags as "-c" and "--casava"; "-c" is ambiguous with the "--contaminants" flag, the program interprets it as --contaminants.
It doesn't recognize non-gzipped files as part of a CASAVA group. When the input files were uncompressed this was the result:
Code:
[kmcarr@titan Sample_Moc-F3]$ fastqc --noextract --nogroup --casava -t 8 *.fastq File 'Moc-F3_ACTTGA_L003_R1_000.fastq' didn't look like part of a CASAVA group File 'Moc-F3_ACTTGA_L003_R1_001.fastq' didn't look like part of a CASAVA group File 'Moc-F3_ACTTGA_L003_R1_002.fastq' didn't look like part of a CASAVA group File 'Moc-F3_ACTTGA_L003_R1_003.fastq' didn't look like part of a CASAVA group File 'Moc-F3_ACTTGA_L003_R1_004.fastq' didn't look like part of a CASAVA group File 'Moc-F3_ACTTGA_L003_R1_005.fastq' didn't look like part of a CASAVA group File 'Moc-F3_ACTTGA_L003_R1_006.fastq' didn't look like part of a CASAVA group File 'Moc-F3_ACTTGA_L003_R1_007.fastq' didn't look like part of a CASAVA group File 'Moc-F3_ACTTGA_L003_R1_008.fastq' didn't look like part of a CASAVA group File 'Moc-F3_ACTTGA_L003_R1_009.fastq' didn't look like part of a CASAVA group File 'Moc-F3_ACTTGA_L003_R2_000.fastq' didn't look like part of a CASAVA group File 'Moc-F3_ACTTGA_L003_R2_001.fastq' didn't look like part of a CASAVA group File 'Moc-F3_ACTTGA_L003_R2_002.fastq' didn't look like part of a CASAVA group File 'Moc-F3_ACTTGA_L003_R2_003.fastq' didn't look like part of a CASAVA group File 'Moc-F3_ACTTGA_L003_R2_004.fastq' didn't look like part of a CASAVA group File 'Moc-F3_ACTTGA_L003_R2_005.fastq' didn't look like part of a CASAVA group File 'Moc-F3_ACTTGA_L003_R2_006.fastq' didn't look like part of a CASAVA group File 'Moc-F3_ACTTGA_L003_R2_007.fastq' didn't look like part of a CASAVA group File 'Moc-F3_ACTTGA_L003_R2_008.fastq' didn't look like part of a CASAVA group File 'Moc-F3_ACTTGA_L003_R2_009.fastq' didn't look like part of a CASAVA group
[Why were the files not gzipped you ask? These weren't files output directly from CASAVA. I had single, large file created by CASAVA 1.8.1 and then used split to simulate segmented output.]
When I accounted for these two issues the output was identical to running FastQC 0.9.6 on a single file containing only the filtered reads.
Comment