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Hello forum,
I am a new SPAdes user (beginner). I am looking for some help with SPAdes syntax for merged PE reads. I merged PE-reads (2X150 bp) using bbmerge. I have original files before merging (R1_trim.fq.gz and R2_trim.fq.gz), merged file (bbmerge output), and umerged_R1.fq.gz and unmerged_R2.fq.gz (bbmerge output). What is the correct syntax for merged reads?
edit: after communicating with moderators. [syntax below]
Note: unmerged_R1.fq.gz and umerged_R2.fq.gz are the leftover unmerged read files (in my case bbmerge output) and merged.fq.gz is merged read file (bbmerge output).
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Hello forum,
I am a new SPAdes user (beginner). I am looking for some help with SPAdes syntax for merged PE reads. I merged PE-reads (2X150 bp) using bbmerge. I have original files before merging (R1_trim.fq.gz and R2_trim.fq.gz), merged file (bbmerge output), and umerged_R1.fq.gz and unmerged_R2.fq.gz (bbmerge output). What is the correct syntax for merged reads?
edit: after communicating with moderators. [syntax below]
spades.py -1 unmerged_R1.fq.gz -2 unmerged_R2.fq.gz --merged merged.fq.gz --careful -o spades_assembly_results
Note: unmerged_R1.fq.gz and umerged_R2.fq.gz are the leftover unmerged read files (in my case bbmerge output) and merged.fq.gz is merged read file (bbmerge output).
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