Question: problem with SeqPrep
0
gravatar for haddadfatiha62
10 weeks 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 • 143 views
ADD COMMENTlink modified 23 days ago by h.mon27k • written 10 weeks 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 10 weeks ago • written 10 weeks ago by genomax71k

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

ADD REPLYlink written 10 weeks 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 10 weeks ago by genomax71k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2015 users visited in the last hour