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Using RATTLE on illumina and nanopore reads #48

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phrh opened this issue May 10, 2023 · 5 comments
Open

Using RATTLE on illumina and nanopore reads #48

phrh opened this issue May 10, 2023 · 5 comments

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@phrh
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phrh commented May 10, 2023

Hello,
I have sequences of RNAseq generated using both nanopore and illumina, I want to know if it is possible to give in input to RATTLE both sets?

Thanks

@EduEyras
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EduEyras commented May 11, 2023 via email

@phrh
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phrh commented May 16, 2023

Thanks for your answer I am going to try, is it possible to give the reads in fasta format to RATTLE?

@eileen-xue
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Hi,

RATTLE can process fasta format inputs. However, we recommend using fastq inputs. Since the error correction and polishing step needs to use the quality values, the results of fasta inputs will be less accurate than fastq.

Cheers,
Eileen

@phrh
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phrh commented May 25, 2023

Hi, it did not work. I tried with the fasta and the fastq, but in both cases, it shows an error terminate called after throwing an instance of 'std::bad_alloc. Is it the number of reads (maximum limit)?

I have an additional question. Can the corrected reads that outputs Rattle, be used in input to obtain clusters as an iterative approach?

@EduEyras
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EduEyras commented May 25, 2023 via email

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