RNA spades trimmomatic not working?

Hi ive tried using RNA spades for my data. So far ive used 26 and 16. Should i be using 11? I know my data is a paired ends interlaced reads i dont know what to data set to use after that.

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Hello @Preet_Kaur

Try running alignments using the post-QA paired reads from Trimmomatic. That would be the dataset collection 33 in the screenshot. The tool form would need to be adjusted to match these settings. Appropriate collections will show up on the form. You collection only has one pair in the list but that’s Ok.



I did that but now i cant seem to click on my data. It says 0 bytes. Should this be in another format?

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Hi @Preet_Kaur

Ok, thanks for trying that. You now have a job that didn’t technically fail (as the original did). That job is now producing no outputs. That could be due to the read content and/or parameter settings. Less likely is some software bug.

Please share back a link to the history and we can help to check for software issues. Please leave all inputs/outputs undeleted, including the upstream QA steps. If you haven’t run FastQC and Fastq Info on the outputs of Trimmomatic yet, please do those first. Sharing your History

url: https://usegalaxy.org/u/p/h/sra-1

Here you go.
Thank you for the help

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Hi @Preet_Kaur

Thanks for sharing the history – you can unshare it now.

The reads you are working with are single end single cell rna-seq. GSM2668223: M3_p1_4; Mus musculus; RNA-Seq - SRA - NCBI

Working with scrna-seq reads require different analysis methods than what you have done so far. The R1 reads are barcodes and the R2 reads are the actual sequenced data. Please review the tutorials below for how to manipulate these types data.

Im actually working with [SRX10084615] CEL-Seq2 of Amphimedon queenslandica: larvae dissociated cell
the SRA number for this is SRR13695362.

Would i still use singe cell for this?