Edena Assembler error

Question

[Abdul Rafay Khan]

I try Edena but i can't get the same length of my reads, If you can help me I appreciated. ... [err] All reads within a file must be the same length.

edena -singleEnd FileName_1.fastq

Rapid file(s) examination... 42 93
[err] All reads within a file must be the same length

[Medhat]

you can get the shortest read in your fasta/q file then trim the rest to be the same length ; but I do not understand why the software behaves in this way, what is the idea of all reads have the same length?

or you can first but a threshold to get all reads greater than length x (for example 100) them trim them all to be 100

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this will give you the length of the least reads length cat file.fastq | awk '{if(NR%2==0) print( length $0);}' | uniq | sort -n | head -n 10

[Abdul Rafay Khan]

cat file.fastq | awk '{if(NR%2==0) print( length $0);}' | uniq | sort -n | head -n 10

30;?+0AD>8CD<G:BCAF;CGF4C<@B99CE
30:;+?0B4CC?CBEECEB@E><C+<ACBEEA
30@@@;+@)0@C>FFB9+<C?EA@;C?@7B?8
30:111AD3=DDFF8B+<:CCAEC<CG<:CAF
30=114A:ABBCF?DAGE9<?DCF9<A<<F:C
30=114A:,AD8:AFF2C@C<@>H4CD<<EHC

What is the least reads length in above result?

[Medhat]

sorry the command should be like

awk '{if(NR%2==0) print( length );}' | uniq| sort | head -n 10 and result will be something like

50 51 52 55 ....

those are the least 10 length of your reads