Hello everyone,
I am new to next-gen sequencing and this forum. Hope someone can help me out here.
To practice and test software tools for alignment, I downloaded a short reads dataset of a yeast genome and tried to convert the sanger-fastq format data to Maq’s BFQ ( I didn't know that SRA provides sanger-format fastq and MAQ prefer the other format of fastq).
Command line I used was
Part of warnings showed on the screen.
I checked the bfq format fastq file by converting it to sanger format fastq. It appears that fastq2bfq can not handle the symbol '@' contained in quality score lines in sanger format fastq files.
I am wondering if anyone have already wrote a sanger-format fastq to illumina-format fastq cnoverter, it will be really helpful to me.
Thanks.
I am new to next-gen sequencing and this forum. Hope someone can help me out here.
To practice and test software tools for alignment, I downloaded a short reads dataset of a yeast genome and tried to convert the sanger-fastq format data to Maq’s BFQ ( I didn't know that SRA provides sanger-format fastq and MAQ prefer the other format of fastq).
Command line I used was
Code:
maq fastq2bfq SRR002051.fastq SRR002051.bfq
Code:
[seq_read_fastq] Inconsistent sequence name: ;E)$$$%%%%$%$""&"""""". Continue anyway. [seq_read_fastq] Inconsistent sequence name: 32-)"""""". Continue anyway. [seq_read_fastq] Inconsistent sequence name: *IDI*II%A;1+3&"""""". Continue anyway. [seq_read_fastq] Inconsistent sequence name: $$,$"#&&%4&+$("""""". Continue anyway. [seq_read_fastq] Inconsistent sequence name: 6&%*I)''%11#"+-"""""". Continue anyway. [seq_read_fastq] Inconsistent sequence name: 43&"""""". Continue anyway. [seq_read_fastq] Inconsistent sequence name: (I#$,)B:E/(&"""""". Continue anyway. [seq_read_fastq] Inconsistent sequence name: I5.=;&#!"-"""""". Continue anyway. [seq_read_fastq] Inconsistent sequence name: """""". Continue anyway. [seq_read_fastq] Inconsistent sequence name: (%%+%$/"""""". Continue anyway. [seq_read_fastq] Inconsistent sequence name: $&/#2#&%!%"!"""""". Continue anyway. [seq_read_fastq] Inconsistent sequence name: /%%!$#%*#"&"""""". Continue anyway. [seq_read_fastq] Inconsistent sequence name: +6+/&%+&%$"""""". Continue anyway. [seq_read_fastq] Inconsistent sequence name: +F)'$5*&+9%""+%"""""". Continue anyway. [seq_read_fastq] Inconsistent sequence name: %%'"!"""""". Continue anyway.
I am wondering if anyone have already wrote a sanger-format fastq to illumina-format fastq cnoverter, it will be really helpful to me.
Thanks.
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