Wild output

[ardmore]

Hello, I am tring to generate the consensus sequence by using command

samtools pileup -cf ref.fa aln.bam | samtools.pl pileup2fq -D100 > cns.fastq

However I found that in the output file there are a lot wild characters such as

~~~~~~~~~~~~~~~~~{~~~~~~~~o~~~~~~~~~~~~{~~~{~~~{{{x{{{~{{xfr
uuurru{{xux{{{{{{{~~~{~~~~~~~f~~n~~~~~~~~~~~~~~~~~~~~~~~~~~~
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~{c{{~x~~~~l{
~~~~~~~~~~~~~xxxxxuuuroloooooollolfffiiifffcfffff``Mc]]]``]`
]`````````cffiifiiiiillllllilllllllill3liiiiiffffffff```````
``]]]]]]]]]]ZZZWWWTTQQNNNNNQTTQEQKEKHEEEEEBBBEEHHHHKKQTWWWWW
QTW]`fiiNllilillllliloolollrrrrrrrrrruuuux{{{{{{~~~~~~~~~~~~

So what is wrong?

[swbarnes2]

You made a fastq, and it has quality scores, exactly like a fastq is supposed to have.

If you understood the programs you are running, you would not be so surprised when they function exactly as they are supposd to.

[ardmore]

I am not strong on perl. So could you please advise me the details?
How can I get the right sequence?

[dpryan]

I am not strong on perl.

You're question has nothing to do with perl.

So could you please advise me the details?
How can I get the right sequence?

swbarnes2 gave you enough to figure it out:

You made a fastq, and it has quality scores, exactly like a fastq is supposed to have.

So ardmore, did you actually read his reply? Have you looked at the fastq file format? Have you bothered looking up what a quality score is?

[ardmore]

Okay. Can we read quality scores based on the fasta file?
I google search but no clue.

[dpryan]

Okay. Can we read quality scores based on the fasta file?
I google search but no clue.

That's not a coherent question. Why are you asking about fasta files when you have a fastq file? I wonder if your problem is misreading fastq as fasta.

[ardmore]

Oop. I did make a mistake. I misread the command. My goal is to get a fasta file. I didn't pay attention to it.

So how can I get the fasta file?
Convert fastq to fasta?
or using mpileup?
Because I got an error by
http://biostar.stackexchange.com/que...ric-in-numeric
I am sad.