Question: problem with SeqPrep
0
gravatar for haddadfatiha62
15 months ago by
haddadfatiha620 wrote:

Hi everybody I want to merge reads (reverse and forward) so i use seqPrep with this command :

 SeqPrep -f ERR770964_1.fastq -r /ERR770964_2.fastq -1 forward.fastq -2 reverse.fastq -s merged_file.fastq

, i got this result

Pairs Processed:        0
Pairs Merged:   1066735
Pairs With Adapters:    12980
Pairs Discarded:        6788

but the output files is not readable ,when i open the merged file i get somthing like this

▒▒ݒ▒J▒-v▒Oqn▒̞▒ĿdI▒▒▒#'▒8▒ ▒▒▒▒a,▒*▒gFs"\▒w▒J▒(▒▒▒▒▒▒▒0▒ƾ▒▒▒O▒▒▒▒▒=▒▒▒p+▒▒▒▒[▒▒▒▒v▒▒1▒Bsk▒▒▒▒▒▒▒▒▒_▒c▒r▒▒▒E▒E▒▒_r&▒(▒▒#▒▒`▒▒~▒▒_I▒p▒;lK_B▒#fMr<▒▒_▒▒Jr▒▒▒bJ9▒^▒▒Ɩ▒▒C]o▒▒zr▒▒▒▒▒&w▒&▒7▒▒▒▒▒▒▒)▒▒>▒▒H▒#[▒k▒▒:~▒▒÷)▒ld#▒▒▒ɹ▒▒▒t[▒_|▒▒▒iN)▒q0▒c▒▒▒O~▒▒▒▒<▒▒▒6C▒Oh▒▒▒▒▒\UU▒▒fZ{▒▒f[▒▒VU{▒▒C▒▒▒+▒▒iJ▒g▒tk▒&▒▒7▒hˇ▒▒▒~▒l)▒▒▒▒O▒▒"u&Xx▒E%Y▒1▒Bq$▒▒5▒.6▒S▒▒Q#▒b▒▒▒▒\▒+▒Gr▒"▒▒▒XV{&▒b▒▒0ڜ▒▒UW▒▒Mߑ▒▒Mi▒v▒▒tLN▒"_▒6[▒s▒▒y▒▒▒vMӖ▒'eG=▒6/vC▒▒▒▒▒-▒4▒▒�▒{▒▒▒ۆBU▒▒>▒▒▒▒▒?i▒▒}▒oT▒▒Y▒'▒▒▒▒/~h▒|▒b▒▒▒D▒▒gWW▒▒T▒▒T▒D▒# ▒▒j▒]▒▒▒Ӕ▒▒l▒▒;▒▒o~▒ please can you help me because i m begeniinng in this field thanks

sequence • 448 views
ADD COMMENTlink modified 14 months ago by h.mon31k • written 15 months ago by haddadfatiha620
1

Even though your file names say .fastq it looks like your files may be compressed/gzipped. What do you get if you do file ERR770964_1.fastq and file ERR770964_2.fastq?

ADD REPLYlink modified 15 months ago • written 15 months ago by genomax91k

My files is not compressed , it's fastq file i don't indrstand when i have problem

ADD REPLYlink written 15 months ago by haddadfatiha620

I asked you to provide output for the two commands above. Without that there is not much we can say.

ADD REPLYlink written 15 months ago by genomax91k

If you are Linux user try zcat merged_file.fastq you can decompress via gunzip merged_file.fastq, then open it

ADD REPLYlink written 9 months ago by Memam0
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