Hello, I performed 6 different runs of Cufflinks using the same Reference Annotation on 6 different samples. I expected the resulting tabular output to be constant given the same Reference Annotation was used each time. What I found is that there was an inconsistency. Specific example, here is top 5 rows from output for one of the six samples: tracking_id class_code nearest_ref_id gene_id gene_short_name tss_id locus length coverage FPKM FPKM_conf_lo FPKM_conf_hi FPKM_status NM_001005484 - - NM_001005484 - - chr1:69090-70008 - - 0 0 0 OK NR_026820 - - NR_026820 - - chr1:34610-36081 - - 0 0 0 OK NM_001005221 - - NM_001005221 - - chr1:367658-368597 - - 0 0 0 OK NR_046018 - - NR_046018 - - chr1:11873-14408 - - 0 0 0 OK Here are top 5 rows from output for another of the six samples: tracking_id class_code nearest_ref_id gene_id gene_short_name tss_id locus length coverage FPKM FPKM_conf_lo FPKM_conf_hi FPKM_status NM_001005484 - - NM_001005484 - - chr1:69090-70008 - - 0 0 0 OK NR_026820 - - NR_026820 - - chr1:34610-36081 - - 0 0 0 OK NM_001005221 - - NM_001005221 - - chr1:367658-368597 - - 0 0 0 OK NR_046018 - - NR_046018 - - chr1:11873-14408 - - 0 0 0 OK NR_024540 - - NR_024540 - - chr1:14361-29370 - - 15114.7 9501.21 20728.1 OK Here are top 5 rows from output for yet another of the six samples: tracking_id class_code nearest_ref_id gene_id gene_short_name tss_id locus length coverage FPKM FPKM_conf_lo FPKM_conf_hi FPKM_status NR_026820 - - NR_026820 - - chr1:34610-36081 - - 0 0 0 OK NM_001005484 - - NM_001005484 - - chr1:69090-70008 - - 0 0 0 OK NM_001005221 - - NM_001005221 - - chr1:367658-368597 - - 0 0 0 OK NR_046018 - - NR_046018 - - chr1:11873-14408 - - 0 0 0 OK NR_024540 - - NR_024540 - - chr1:14361-29370 - - 28376.8 20008.9 36744.6 OK As a user, when selecting the same Reference Annotation to be used. I would expect the index of results by tracking id to be the same. Why is this happening? Why are they not consistent? If were to concat the above results across samples without correcting the indices, my data would be all mixed up. I bring this to your attention as someone may not correct the indices before concat and therefore would be doing downstream analysis incorrect concatted data. In turn, I would recommend that the index of results be corrected to be constant for a Reference Annotation when selected. Thank you in advance for this consideration. Best, Kory Johnson -------------------------------------------- Kory R. Johnson, MS, PhD Sr. Bioinformatics Scientist [cid:image001.jpg@01CD074F.C0C74CB0] www.kellygovernmentsolutions.com Providing Contract Services For: Bioinformatics Section, Information Technology & Bioinformatics Program, Division of Intramural Research (DIR), National Institute of Neurological Disorders & Stroke (NINDS), National Institutes of Health (NIH), Bethesda, Maryland Mailing Address: NINDS/NIH Clinical Center (Building 10) Office 5S223 9000 Rockville Pike Bethesda, MD 20892 Contact Information: Phone: 301-402-1956 Fax: 301-480-3563 email: johnsonko@ninds.nih.gov P Green Message: Please consider the environment before printing this e-mail. Thank you. Important Message: This electronic message transmission contains information intended for the recipient only. Such that, the information contained herein may be confidential, privaledged, or proprietary. If you are not the intended recipient, be aware that any disclosure, copying, distribution, or use of this information is strictly prohibited. If you have received this electronic information in error, please notify the sender immediately by telephone. Thank you. --------------------------------------------
