HomeCLC software: Important notificationsIssues affecting only versions of products released prior to June 2017Basespace fastq files imported using Solid Fastq importer reports incorrect sequences

3.10. Basespace fastq files imported using Solid Fastq importer reports incorrect sequences

Summary

Base space fastq files imported using the SOLiD Fastq importer of the CLC Genomics Workbench 8.0 and earlier, or the CLC Cancer Release Workbench 2.0 and earlier results in Sequence Lists with incorrect sequence data. We are very sorry for any inconvenience this has caused.

Who is affected

Anyone who has imported a base space fastq file using the tool: Import | SOLiD and then has chosen a base space fastq file to import using this tool in the CLC Genomics Workbench 8.0 and 7.5.2 and earlier, and the CLC Cancer Release Workbench 2.0 and 1.5.3 and earlier. This issue does not affect import of fastq files in color space.

What are the symptoms?

The Sequence List will report sequences that are not correct. If you use a text reading program to look at the top of your basespace fastq file, you will be able to see that the sequences there do not resemble sequences of the same name, if you chose to keep names on import, in the sequence list. If you did not choose to keep names on import, then the sequences should be in the same order as in your original fastq file if it was single data. For paired data, the first sequence should be the first sequence in one of your two fastq files. It is anticipated that you will see that the top sequence does not match either of these.

When will this be fixed?

This issue has been fixed in the CLC Genomics Workbench 7.5.3, the CLC Genomics Workbench 8.0.1, the CLC Cancer Workbench 1.5.4 and the Biomedical Genomics Workbench 2.1, released in April, 2015.

 

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