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Understanding the results from converting fasta files to fastq files using reformat.sh from bbsuite

Hi , I tried to edit fastA file to fastq file using the command from this A: Edit format from .fa to .fq. im trying to interpret the results now. used a fake qscore of 35. The seequences in the fasta file had A,C,G,T,N... For example if the fasta file is in the format 

>N33.01
ACTTTCGTCTTNNNNNNNNNNNNNNNN

Then the fast qfile produced was in the format

>N33.01
ACTTTCGTCTTNNNNNNNNNNNNNNNN
+
DDDDDDDDDDD!!!!!!!!!!!!!!!!

so after running reformat.sh from bbsuite i get a fast q file with ! at the positions with N and D at positions with basecall(A,C,G,T). can someone explainhow it assigns the values based on a fake qscore 35.

Is the bases A,C,G,T with is represented as D in fast qfile has a quality score of 35 ? then what does the (!) at position of Ns represent.

sequence sequencing genome gene
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written by a4appy23 • a4appy23

There should be no commas in either fastA or fastQ, did you introduce them?

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written by ATpoint ATpoint

1 answer

Since N represents a no call, bbmap is assigning a Q-score of 0 to those bases.

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written by GenoMax GenoMax

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