How To Convert And Filter Scf Format Into Fasta?

Question

[Nickengland]

If I have a large number of files in SCF format, and want to batch convert them into Fasta format, (after filtering for quality scores of base calling to trim) what is the standard tool to convert them? I have installed Staden Package iolib, but it seems to have only scfinfo, scfdump and scfupdate to do with scf files which don't seem to do what I want.

scf_dump takes you to a text based file (although I am unsure of the format) is there another program to convert this to .fasta with a quality score filter?

[Edit] Using the http://staden.sourceforge.net/overview.html pregap4 program you can specify a quality threashold to mark to ignore, and export a sequence using qclip and extract_seq, but the sequences extracted in this way don't seem to include the filtering step. Does anyone know why? Seems the filter might just mark bases as ignored, but the extractor doesn't obey this?

Answer 1

[Nickengland]

It appears the problem I was having was failing to initialise the experimental files properly for pregap4 to work.

The complete sequence of events should be: run init_exp to convert the SCF files into .exp files run qclip to append information on where the sequence should be clipped to the .exp files run extract_seq to obtain a .fasta file out of your .exp files with the sequence properly clipped.

I hope this helps anyone else trying to perform this operation!

You cause either run the programs above, or run pregap4 which has a gui to configure things. Bare in mind that the init_exp module must be run before qclip or extract_seq from this tool or it will fail without any usefull error messages!

Answer 2

[Ian]

There is a set of Perl libraries SeqIO that can convert SCF to FASTQ (fasta + asci encoded quality scores).

The last contribution of this BioStars thread may help.

I hope there is something of use here for you.

Answer 3

[lh3]

Not all SCF files keep the base calls. In that case, you need phred to do base calling.

[BioApps]

If the base calls are not stored in the SCF file, then not the SCF file (format) itself is faulty. It is the program that made the conversion. Well... assuming that the original file (for ex ABI) had the base calls included.