Eland Multi

File format

  1. Sequence Name
  2. Sequence
  3. One of NM, QC, RM or the following:
  4. x:y:z where x,y,z are the number of exact, 1-mismatch, and 2-mismatch matches.
  5. blank if no matches found, or if too many matches found or the following:
    • chr1.fa:1234R1,2345F the first value is the fasta file name, the 1234R1 is indicates the location 1234, and strand R

Eland Extended

Eland extended is like the eland multi format, except after the location, there's a bit of information about which bases didn't match and what the genomic value was.

Eland result

... document later.

Converting Eland Files

If you have some kind of eland result file but want a sequence file (fasta), you can convert them by doing something like:

result2sequence.py

#!/usr/bin/env python
import sys

for line in sys.stdin:
    record = line.split('\t')
    print "%s" % (record[0],)  # first column is the header
    print "%s" % (record[1],)  # second column is the sequence

and then doing:

cat s_4_eland_result.txt | python result2sequence.py > s_4_sequence.txt

Bug Tracking Project Management

ElandExtended (last edited 2010-09-08 16:16:59 by 95-65-50-150)