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Old 12-06-2012, 12:30 PM   #1
Anthony.287
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Location: Ohio

Join Date: Dec 2010
Posts: 95
Default RLMIDs vs GSMIDs

Hello all!
I'm finally starting to get the hang of sfffile, and am finding some things that I can't explain. For instance, one particular region (a pool of 4 RLMID tagged rapid libraries) on the most recent PTP had 43,949 reads. 43,792 of those got sorted in sff's based on the RLMIDs. Out of curiosity, I sorted using the GSMIDs, and ~15,000 were sorted then. What could be happening?

[[email protected] ~]$ sfffile -s GSMIDs /data/R_2012_11_29_16_12_43_FLX05100626_Administrator_Shotgun/sff/HYPJBHH12_Shotgun.sff
Reading the input SFF file(s)...
Generating the split SFF file(s)...
MID1: 3 reads written into the SFF file.
MID2: 0 reads found.
MID3: 13 reads written into the SFF file.
MID4: 10898 reads written into the SFF file.
MID5: 4660 reads written into the SFF file.
MID6: 0 reads found.
MID7: 0 reads found.
MID8: 0 reads found.
MID9: 1 reads written into the SFF file.
MID10: 0 reads found.
MID11: 0 reads found.
MID12: 0 reads found.
MID13: 0 reads found.
MID14: 0 reads found.
[[email protected] ~]$ sfffile -s RLMIDs /data/R_2012_11_29_16_12_43_FLX05100626_Administrator_Shotgun/sff/HYPJBHH12_Shotgun.sff
Reading the input SFF file(s)...
Generating the split SFF file(s)...
RL1: 24344 reads written into the SFF file.
RL2: 11022 reads written into the SFF file.
RL3: 3692 reads written into the SFF file.
RL4: 4734 reads written into the SFF file.
RL5: 0 reads found.
RL6: 1 reads written into the SFF file.
RL7: 0 reads found.
RL8: 0 reads found.
RL9: 0 reads found.
RL10: 0 reads found.
RL11: 0 reads found.
RL12: 0 reads found.


Can the RLMIDs be misinterpreted as GSMIDs, and vice-versa? Any ideas?

Thank you!
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