Have anyone tried Correction package of SOAPdenovo? I input the fq file, but it alway said that fail to open file?
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Dear Elisa,
you have to provide KmerFreq with a text file containing the names of the sequence file(s), otherwise it will try to open every line as a file name.
So like
Enjoy!Code:KmerFreq -i filenames.txt -o kmer_table
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I have put the name of file in the txt file like this:
/diag/home/jjin/oil_palm/raw/DNA1.fastq
/diag/home/jjin/oil_palm/raw/DNA2.fastq
However, it still display error for the second file:
quality cutoff: 5
seed length: 17
output kmer index?: no
file format: fq
>>>>>>>>>>hash initializing<<<<<<<<<<
in /diag/home/jjin/oil_palm/raw/DNA1.fastq
file of the reads - /diag/home/jjin/oil_palm/raw/DNA2.fast - opening failed.
spend total time 3919
Can anyone give me some suggestions?
Thanks!
JingjingComment
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I met the same problem as yours. Just add an 'return' at the end of second line of the input list file. It will be fine! Hope this will help you!
Originally posted by jjjscuedu View PostComment
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I don't want to sound like a jerk, but did you make sure the path and permissions were correct?
Originally posted by jjjscuedu View PostComment
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NGS has revolutionized clinical microbiology by offering new ways to identify and surveil pathogens without prior knowledge of the target. One popular approach is 16S rRNA and ITS amplicon sequencing, which targets specific microbial markers. But studies are increasingly incorporating shotgun metagenomics, a technique that sequences all DNA from a sample without targeting specific microbial markers. This approach allows more detailed taxonomic classification,...10-30-2026, 06:46 AM
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