Using RATTLE on illumina and nanopore reads

[phrh]

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]

Thanks for the question It might work since rattle prioritises longer reads to build clusters. The rattle algorithm then assumes that two reads originate from the same cluster if they share enough k-mers. So I reckon that short reads will be mosty added to existing clusters. If you try it, please let me know how it goes Thanks E

On Thu, 11 May 2023 at 02:26, phrh ***@***.***> wrote: 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 — Reply to this email directly, view it on GitHub <#48>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ADCZKB34UCXBLO246VQV3GDXFO6SPANCNFSM6AAAAAAX463TYE> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

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[phrh]

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

[eileen-xue]

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]

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]

How many reads are you using? It could also be some reads being too short or too long. You could try limiting those. Yes, you can definitely use the corrected reads to run again the first clustering step. I hope this helps Eduardo

On Fri, 26 May 2023 at 00:58, phrh ***@***.***> wrote: 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? — Reply to this email directly, view it on GitHub <#48 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ADCZKB4KA54JKZ7JUHXUURLXH5XQFANCNFSM6AAAAAAX463TYE> . You are receiving this because you commented.Message ID: ***@***.***>

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