Hi,
I am using SRA reads to identify the roles of the intergenic regions I have isolated using the perl script. I have very moderate understanding of the output and purposes of different tools. So far I used bowtie to align the SRA reads to my reference genome and then cufflinks to get the expression value for each gene. I do not understand now how can I relate the intergenic regions to the SRA read expression output of cufflinks.For cufflinks I have four output as:genes.fpkm_tracking isoforms.fpkm_tracking skipped.gtf transcripts.gtf
For my understanding I looked for the expression value of genes.fpkm_tracking. Now from this point I do not have any idea how to relate my output to the intergenic regions. My genes.fpkm_tracking output looks like this:
gene0 - - gene0 - - NC_000921.1:50-467 - - 9.31549 6.41812 12.2129 OK
gene1 - - gene1 - - NC_000921.1:468-939 - - 5.89251 3.80506 7.97995 OK
CUFF.1 - - CUFF.1 - - NC_000921.1:948-2431 - - 23.5725 20.3547 26.7902 OK
gene27 - - gene27 - - NC_000921.1:26314-27595 - - 52.0518 48.7694 55.3342 OK
CUFF.2 - - CUFF.2 - - NC_000921.1:27752-31609 - - 54.1168 48.789 59.4447 OK
CUFF.3 - - CUFF.3 - - NC_000921.1:29641-31999 - - 0 0 0 OK
gene32 - - gene32 - - NC_000921.1:32110-32524 - - 3.58937 1.79469 5.38406 OK
CUFF.4 - - CUFF.4 - - NC_000921.1:32525-35369 - - 20.8448 14.6654 27.0242 OK
CUFF.5 - - CUFF.5 - - NC_000921.1:35371-37741 - - 12.1854 10.3385 14.0322 OK
CUFF.6 - - CUFF.6 - - NC_000921.1:37756-44757 - - 6.01506 4.82217 7.20795 OK
gene46 - - gene46 - - NC_000921.1:44708-45005 - - 0 0 0 OK
gene47 - - gene47 - - NC_000921.1:45189-46188 - - 0.615931 0.20531 1.02655 OK
CUFF.7 - - CUFF.7 - - NC_000921.1:46190-49432 - - 9.48516 8.15957 10.8108 OK
CUFF.8 - - CUFF.8 - - NC_000921.1:49490-50718 - - 5.19769 3.40986 6.98552 OK
gene52 - - gene52 - - NC_000921.1:51151-52183 - - 21.3319 18.946 23.7178 OK
gene53 - - gene53 - - NC_000921.1:52192-52975 - - 6.08926 4.5605 7.61801 OK
gene54 - - gene54 - - NC_000921.1:53402-54893 - - 82.8641 79.0848 86.6433 OK
gene55 - - gene55 - - NC_000921.1:54919-58477 - - 12.9985 12.0592 13.9377 OK
gene56 - - gene56 - - NC_000921.1:58797-59007 - - 1128.22 1063.83 1192.61 OK
gene57 - - gene57 - - NC_000921.1:59334-59997 - - 0 0 0 OK
gene58 - - gene58 - - NC_000921.1:60126-60489 - - 0 0 0 OK
gene59 - - gene59 - - NC_000921.1:60489-61473 - - 2.5784 1.72187 3.43493 OK
gene60 - - gene60 - - NC_000921.1:61483-61915 - - 0 0 0 OK
gene61 - - gene61 - - NC_000921.1:62095-63664 - - 0 0 0 OK
gene62 - - gene62 - - NC_000921.1:63897-64467 - - 0.280373 0 0.677432 OK
gene63 - - gene63 - - NC_000921.1:64482-64743 - - 0 0 0 OK
CUFF.9 - - CUFF.9 - - NC_000921.1:64753-66645 - - 0.256232 0 0.61988 OK
CUFF.10 - - CUFF.10 - - NC_000921.1:66649-69413 - - 0 0 0 OK
CUFF.11 - - CUFF.11 - - NC_000921.1:71719-76714 - - 118.293 112.861 123.725 OK
CUFF.12 - - CUFF.12 - - NC_000921.1:69486-77636 - - 0 0 0 OK
gene78 - - gene78 - - NC_000921.1:77725-77995 - - 22.9369 16.2247 29.6491 OK
gene79 - - gene79 - - NC_000921.1:78113-79172 - - 45.6573 42.2265 49.0881 OK
Please, help me with this. Regards, Bandana
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bandanaschapagain •
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To me it's unclear what you aim to achieve... Perhaps you should read the manual and follow a tutorial to get a better idea of what you are doing and what the purpose of the tools is.