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How to make a paired-end reverse file

I had the two files paired, however, I lost what contained the reverse reads. Is there any way to redo this lost file using only file 1 (foward)? Sorry for ignorance, I'm new to this area. I need the file to do the metagenomic assembly using Spades (metaspades), which needs these 2 files (forward and reverse).

assembly next-gen
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updated by h.mon h.mon • written by fb_marinho88 • fb_marinho88

2 answers

By "lost" you mean you deleted the file with R2 (reverse) reads? If so, no, you can't recover this data, it is gone forever. You will have to assemble the genome using the R1 as single-end reads, with the parameter -s file_R1.fastq.

But if by "lost" you mean you converted your R1 and R2 files into an interleaved fastq file, then you can feed SPAdes with this file, using the parameter --12 file_interleaved.fastq.

If you deleted the file, you can try to contact the sequencing provider and ask if they still have the files stored.

edit: Actually, it seems metaSPAdes does not support single reads, see genomax comment bellow. You may try to use it, but I am not certain it will work. You may contact the developers and ask about this, they are really responsive.

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written by h.mon h.mon

Thank you! I'll mount it using -s file_R1.fastq =D

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written by fb_marinho88 • fb_marinho88

Check the current manual for metaSPAdes but at least v. 3.12.0 manual has this requirement

Currently metaSPAdes supports only a single short-read library which has to be paired-end (we hope to remove this restriction soon).

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written by GenoMax GenoMax

You are right. The command-line help fooled me:

metaspades -h

-s <filename> file with unpaired reads

In this case, I suggest you look into MEGAHIT.

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written by h.mon h.mon

You really can't contact the sequencing provider / collaborator and ask for a copy of the data?

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written by h.mon h.mon

Unfortunately not.They no longer have the file.

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written by fb_marinho88 • fb_marinho88

I lost what contained the reverse reads. Is there any way to redo this lost file using only file 1 (foward)?

If lost refers to permanent loss of data (e.g. deletion/corruption of the file) then there is nothing you can do to recreate the file. You will need to ask your sequence provider to provide you with a new copy.

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written by GenoMax GenoMax

=/ Sad ! Is there any way to do the assembly without this file?

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written by fb_marinho88 • fb_marinho88

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