Get the original read IDs from corrected reads by AllPaths-LG error correction module (ErrorCorrectReads.pl)

Question

[emmaielle]

Hi,

I was wondering how can I get the original IDs of the corrected reads with ErrorCorrectReads.pl, because I need the original coordinates of those reads to perform MarkDuplicates.jar and AddOrReplaceReadGroups.jar from Picard.

After performing ErrorCorrectReads, I have as output two fastq with each pair of corrected reads, with their IDs changed, a fastq with the interleaved reads, a fastq with the unpaired reads, and finally a file with the id correlations that looks like this:

#New_ID,  Original_ID
0,  0
1,  1
2,  2
3,  3
4,  4
5,  5
6,  6
7,  7
8,  8
9,  9
10,  11
11,  12
12,  14
...

But the "original_ID" field is barely the position in the input file of that read (i.e.: New ID named "read:0" is the read that on the original file is at position 0 too).

I need the original information, to get the extra info that the name of the read has got. Does anyone have an idea of how to do that/have done it already?

Thanks so much!