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Thanks, yes it's definitely a problem with the FASTQ file. It looks like whoever filtered this data before I got my hands on it was using grep to looks for flags in the identifier and pulls out 4 lines of context around it. But obviously something went very wrong. Now, I just need to hunt down the raw data. Thanks.
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Originally posted by turnersd View PostI've had a problem with FASTQC.
As Dario says, you'll need to track back and work out what went wrong in the creation of this file. It could be as simple as a data corruption on disk or when copying the file.
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Originally posted by turnersd View PostHow would I get rid of these "empty" reads?
Dario
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FASTQC problem on read with no sequence data
I've had a problem with FASTQC. I get the following error:
Code:Failed to process file 0618107SM.fastq uk.ac.bbsrc.babraham.FastQC.Sequence.SequenceFormatException: Midline 'CAAACATACAGCTTAAAAC AACAGACATTTATTATCTTATGGT' didn't start with '+'
Code:@HWUSI-EAS1758R:33:64PA7AAXX:4:1:6103:1039 1:N:0: CTCGATCCACAAACCGCCCTTGGGGTAAACATTCGG + IIIIIIIIIIIIIIIIHIIIIIIIIEHIGHHHHIII @:701;5677@<5@###################### @HWUSI-EAS1758R:33:64PA7AAXX:4:1:6397:1046 1:N:0: CCTTAGGTTATTTCATGCCTAGAAATGTATCCTACA + HHGHHHGHHDHHHHHH@HHHHHHHHHHGHHHHGHHG @HWUSI-EAS1758R:33:64PA7AAXX:4:1:6580:1044 1:N:0: GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTGAAA + GGGGEGDDGBHGHHHEGDGEGGD@GBB???GBGDBF
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The complexity of cancer is clearly demonstrated in the diverse ecosystem of the tumor microenvironment (TME). The TME is made up of numerous cell types and its development begins with the changes that happen during oncogenesis. “Genomic mutations, copy number changes, epigenetic alterations, and alternative gene expression occur to varying degrees within the affected tumor cells,” explained Andrea O’Hara, Ph.D., Strategic Technical Specialist at Azenta. “As...-
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