Is this the correct code for SPades (WGS)?
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2.3 years ago
Princy ▴ 60

Hello, I am using this code for one project Id (Illumina HiSeq 2000 paired end) of bitter melon which has 230 fastq files. so I am running this script separately for each paired-end read. pl let me know if I am using wrong.

spades.py -t 30 --careful -1 ERR44_1.fastq -2 ERR44_2.fastq -o /cabinfs/home/princy889/PRJEB24033_WGS/output_spade/ERR44

Is the --careful parameter necessary?

Fastq Spades WGS • 876 views
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Are you asking How do I run spades on all 230 fastq pairs in an automated fashion?

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no sir, I am asking the parameters that I am using.

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Hello Princy - why did you delete this post?

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Hello, I deleted this post because my query was solved so I thought I should delete the post from here.

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You should not delete the post because your issue was resolved. Instead, add an answer explaining what the problem was and how you resolved it, and accept this answer so people that run into similar problems can refer to your experience. If people here gave you feedback (comments, answers) and that helped you resolve the issue, upvote their posts and interact with them. One day, even you may run into the same problem and forget how you solved it the last time - it happens to all of us. On that day, you'd be glad to have had your experience documented.

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