back to binary

[Layla]

I converted a binary out.map file after a maq alignment to .txt and filtered for unreliable data. Attempting to do a maq pileup on the cleaned data, but pileup requires a .map file.

How do you get a .txt file back into a .map (binary) to do the ./maq pileup or is there a way to do pileup with .txt file?

L

[jnfass]

Hi Layla,

How exactly did you convert the out.map file to text? A custom script? But in that case, you would probably know the format of the binary file ... and probably not need to ask the question you're asking.

confused,
~Joe

[Layla]

Thanx for your reply.
I used the inbuilt command in maq:
./maq mapview out.map > out.txt ---> QC and filter
The pileup cannot accept the out.txt file I have cleaned up. It requires a binary.map file.

[zee]

Why not just grab the reads from your QC filtered file, convert them to fastq using a perl script, then re-align them with MAQ to create a new .map file if you absolutely have to have the data in binary format.

Thanx for your reply.
I used the inbuilt command in maq:
./maq mapview out.map > out.txt ---> QC and filter
The pileup cannot accept the out.txt file I have cleaned up. It requires a binary.map file.