Question: How to make a paired-end reverse file
0
gravatar for fb_marinho88
10 weeks ago by
fb_marinho880 wrote:

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).

next-gen assembly • 187 views
ADD COMMENTlink modified 10 weeks ago by h.mon20k • written 10 weeks ago by fb_marinho880
1
gravatar for h.mon
10 weeks ago by
h.mon20k
Brazil
h.mon20k wrote:

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.

ADD COMMENTlink modified 10 weeks ago • written 10 weeks ago by h.mon20k

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

ADD REPLYlink written 10 weeks ago by fb_marinho880
1

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).

ADD REPLYlink modified 10 weeks ago • written 10 weeks ago by genomax57k

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.

ADD REPLYlink modified 10 weeks ago • written 10 weeks ago by h.mon20k

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

ADD REPLYlink written 10 weeks ago by h.mon20k

Unfortunately not.They no longer have the file.

ADD REPLYlink written 10 weeks ago by fb_marinho880
0
gravatar for genomax
10 weeks ago by
genomax57k
United States
genomax57k wrote:

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.

ADD COMMENTlink written 10 weeks ago by genomax57k

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

ADD REPLYlink written 10 weeks ago by fb_marinho880
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