Eland_Result.Txt To "Eland_Sorted.Txt"/Sam

Question

[avalanche]

I currently have an alignment file in the "eland_result.txt" format (as shown below):

HWI-EAS107_3:3:1:226:301 AGCCATAATGTGAGAGAGTGTAACTTCTTCAGT NM 0 0 0

HWI-EAS107_3:3:1:237:600 ACTCCAGGTGTACATCAGGCTCACAGGTGGACA R0 2 3 0

HWI-EAS107_3:3:1:122:726 ACAGTCAAAGCTTCAAAAATCTTGGTGTGCCCA U0 1 0 0 chrX.fa 8020122 R ..

HWI-EAS107_3:3:1:189:665 AAATTAGCTGGGCATGTTGGTATGTGCCTGTCA R1 0 4 129

HWI-EAS107_3:3:1:64:354 AAATAACTCTCCCCATTATTCTTGACCAACGTT U0 1 0 0 chr3.fa 89017297 R ..

HWI-EAS107_3:3:1:158:624 AGCTAGGCGCCTGCTCTCGGCGCTTTCCATCCT NM 0 0 0

HWI-EAS107_3:3:1:123:494 AGATGATTCTAGATCATGGAACATGATATAGAT U0 1 2 0 chrX.fa 134805851 F ..

HWI-EAS107_3:3:1:174:571 ACAACGCCCCTCTCGGCGGGGCGCTCCTTGGGG NM 0 0 0

HWI-EAS107_3:3:1:166:367 AACATTCCAAGTGACCGAATGACTTAGCGTTCG NM 0 0 0

HWI-EAS107_3:3:1:238:528 ACGGTTGCAACCCCTGGCTTTTTCTGGTTTCCC U0 1 0 0 chr6.fa 50421707 R ..

I wish to use USEQ's ELANDParser program to parse this file. But I found out that this parser can only accept files in the "elandexport.txt" or "elandsorted.txt" format. When I use this parser with the above "eland_result.txt" file, I get an error saying:

"Line does not contain enough columns".

So I'd like to know whether there is any utility that can help me convert the above "elandresult.txt" format to "elandexport.txt" format ?

If not, is there is any utility to convert "eland_result.txt" to SAM format so that I can probably use USEQ's SAM Parser later on ?

Thank you.

Answer 1

[Alf]

By looking here http://ccg.vital-it.ch/chipseq/elandformat.html the answer is exactly the error you get: "there are no enough columns". The Eland parser is waiting for a file with 12 columns and you are giving a file with 6-8. Nothing more could be said here...

[Swbarnes2]

Among other things, there should be a column for the quality string, you don't have that.