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co-assemble Merged reads using Megahit

Hi everyone,

I have 13 RNA seq datasets (demultiplexed fastq files) and I am trying to co-assemble them into contigs that are at least 1000 kb long and eventually perform a differential transcriptome analysis.

For start, I did a quality check with "illumina-utils" package and merged the reads with zero mismatch. Now I need to co-assemble them and obtain Contig files, fro which I've been advised to use Megahit.

Based on the Megahit tutorials, the input for co-assembly is supposed to be R1.fastq and R2.fastq, i.e. paired-end fastq files from different samples. However, what I have now (after the quality filtering and merging the overlapping pairs) is a bunch of *MERGED files for each sample.

I was wondering if Megahit can still be used for co-assembling already-merged reads or does it have to be pair-end files.

I'm quite new and crawling in the complex world of bioinformatics so any help/advice would be much appreciated.And please let me know if my question is not clear enough.

Cheers, Navid

rna-seq assembly sequence megahit merged-reads
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written by NAVID.BAVI • NAVID.BAVI

I am not familiar with Megahit but perhaps you just need to use your original reads before they were merged. Megahit may do the merging itself as a part of its workflow. Have you looked at the manual/tutorial for Megahit?

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written by GenoMax GenoMax

Thank you for replying. I do need to exclude the reads with mismatch before using Megahit. h.mon comment actually worked.

Cheers Navid

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written by NAVID.BAVI • NAVID.BAVI

h.mon comment worked. Thank you all!

Cheers Navid

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written by NAVID.BAVI • NAVID.BAVI

1 answer

If all you fastq are now merged, i.e., they are now single-end, use the -r parameter. You can combine -1, -2 and -r if you have a mix of merged and unmerged reads.

  Input options that can be specified for multiple times (supporting plain text and gz/bz2 extensions)
    -1                       <pe1>          comma-separated list of fasta/q paired-end #1 files, paired with files in <pe2>
    -2                       <pe2>          comma-separated list of fasta/q paired-end #2 files, paired with files in <pe1>
    --12                     <pe12>         comma-separated list of interleaved fasta/q paired-end files
    -r/--read                <se>           comma-separated list of fasta/q single-end files
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written by h.mon h.mon

Thanks a lot, it worked! I actually missed this point from the manual. My very best, Navid

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written by NAVID.BAVI • NAVID.BAVI

If an answer was helpful, you should upvote it; if the answer resolved your question, you should mark it as accepted. You can accept more than one if they work.
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written by GenoMax GenoMax

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