Closed hcph closed 3 years ago
... it seems like you didn't send any description of your issue here.
Yes, sorry. because the internet here is not good, and these days I cannot open the github properly. Actually, my question is that when I using zUMIs to analysis the data generate from 10 genome (SRR12340620), and the error comes "exiting because of FATAL ERROR in reads input: short read sequence line: 0 Read Name=@SRR12340620.30185066". I has checked the fastq file, that reads exited. Could you please help me to fix this problem?
At 2021-03-20 06:36:30, "cziegenhain" @.***> wrote:
... it seems like you didn't send any description of your issue here.
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Please review the documentation on how to reprocess data from SRA: https://github.com/sdparekh/zUMIs/wiki/Reprocessing-of-public-data
Please review the documentation on how to reprocess data from SRA: https://github.com/sdparekh/zUMIs/wiki/Reprocessing-of-public-data
ok, thank you very much.
Please review the documentation on how to reprocess data from SRA: https://github.com/sdparekh/zUMIs/wiki/Reprocessing-of-public-data
Hello cziegenhain. I reprocessed the public data as you recommend, i.e, use fastq-dup --split file --origfmt --defline-qual '+' x.sra --gzip to unzip the sra data, and run the zUMIs.sh again. While the error comes "pigz:skipping:/.temMerge/SRR12340621_3.fastqSRR12340621ai.gz does not exist @ A00261:171:hl3ftdsxx:4:2653:22797:26694 Error! Fastq files are not in the same order ..............". Bug your reply again. Thanks!
The error suggests that your read files are not in the same order. Please have both your fastq files sorted by readid in the same order.
The error suggests that your read files are not in the same order. Please have both your fastq files sorted by readid in the same order.
Thanks. Now I fix it using this way: seqkit seq --name --only-id SRR12340622_2.fastq.gz SRR12340622_3.fastq.gz | sort | uniq -d >id.txt seqkit grep --pattern-file id.txt SRR12340622_2.fastq.gz -o SRR12340622_S1_L001_R1_001.fq.gz seqkit grep --pattern-file id.txt SRR12340622_3.fastq.gz -o SRR12340622_S1_L001_R2_001.fq.gz
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