miRNA-Seq files header and expression values

na_sd · 11-11-2015, 09:08 AM

I have downloaded miRNA seq file from GSE31617
Files contain information like following:

hsa-let-7a-1 hsa-let-7a t0000020 25073 37013 5p TGAGGTAGTAGGTTGTATAGTT TGAGGTAGTAGGTTGTATAGTT S
hsa-let-7a-1 hsa-let-7a* t0059321 6 12 3p CTATACAATCTACTGTCTTTC CTATACAATCTACTGTCTTTC S
hsa-let-7a-2 hsa-let-7a t0000020 25073 37025 5p TGAGGTAGTAGGTTGTATAGTT TGAGGTAGTAGGTTGTATAGTT S
hsa-let-7a-2 hsa-let-7a-2* t1103419 1 1 3p CTGTACAGCCTCCTAGCTTTCC CTGTACAGCCTCCTAGCTTTCC S
hsa-let-7a-3 hsa-let-7a t0000020 25073 37128 5p TGAGGTAGTAGGTTGTATAGTT TGAGGTAGTAGGTTGTATAGTT S
hsa-let-7a-3 hsa-let-7a* t0059321 6 12 3p CTATACAATCTACTGTCTTTC CTATACAATCTACTGTCTTTC S
hsa-let-7b hsa-let-7b t0000335 3748 7938 5p TGAGGTAGTAGGTTGTGTGGTT TGAGGTAGTAGGTTGTGTGGTT S
hsa-let-7b hsa-let-7b* t0163422 2 2 3p CTATACAACCTACTGCCTTCC CTATACAACCTACTGCCTTCCC D
hsa-let-7c hsa-let-7c t0000721 2095 3068 5p TGAGGTAGTAGGTTGTATGGTT TGAGGTAGTAGGTTGTATGGTT S
hsa-let-7d hsa-let-7d* t0056459 6 18 3p CTATACGACCTGCTGCCTTTC CTATACGACCTGCTGCCTTTCT D
hsa-let-7d hsa-let-7d t0004262 320 767 5p AGAGGTAGTAGGTTGCATAGTT AGAGGTAGTAGGTTGCATAGTT S

First, I wanna know what is the header of columns? (files do not have any header line)
Second, I would like to calculate expression values for miRNAs, how can I do it?
Thanks

PS. I am new in miRNAseq files.

GenoMax · 11-11-2015, 09:15 AM

For ref Cross-posted: https://www.biostars.org/p/165320/

I am thinking that it is some sort of alignment format but the exact name is eluding me (and my google-fu for now). Hopefully some one else will be able to recollect.

Where exactly did you get that data file from on SRA?

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11-11-2015, 09:08 AM	#1
na_sd Junior Member Location: USA Join Date: Nov 2015 Posts: 3	miRNA-Seq files header and expression values I have downloaded miRNA seq file from GSE31617 Files contain information like following: hsa-let-7a-1 hsa-let-7a t0000020 25073 37013 5p TGAGGTAGTAGGTTGTATAGTT TGAGGTAGTAGGTTGTATAGTT S hsa-let-7a-1 hsa-let-7a* t0059321 6 12 3p CTATACAATCTACTGTCTTTC CTATACAATCTACTGTCTTTC S hsa-let-7a-2 hsa-let-7a t0000020 25073 37025 5p TGAGGTAGTAGGTTGTATAGTT TGAGGTAGTAGGTTGTATAGTT S hsa-let-7a-2 hsa-let-7a-2* t1103419 1 1 3p CTGTACAGCCTCCTAGCTTTCC CTGTACAGCCTCCTAGCTTTCC S hsa-let-7a-3 hsa-let-7a t0000020 25073 37128 5p TGAGGTAGTAGGTTGTATAGTT TGAGGTAGTAGGTTGTATAGTT S hsa-let-7a-3 hsa-let-7a* t0059321 6 12 3p CTATACAATCTACTGTCTTTC CTATACAATCTACTGTCTTTC S hsa-let-7b hsa-let-7b t0000335 3748 7938 5p TGAGGTAGTAGGTTGTGTGGTT TGAGGTAGTAGGTTGTGTGGTT S hsa-let-7b hsa-let-7b* t0163422 2 2 3p CTATACAACCTACTGCCTTCC CTATACAACCTACTGCCTTCCC D hsa-let-7c hsa-let-7c t0000721 2095 3068 5p TGAGGTAGTAGGTTGTATGGTT TGAGGTAGTAGGTTGTATGGTT S hsa-let-7d hsa-let-7d* t0056459 6 18 3p CTATACGACCTGCTGCCTTTC CTATACGACCTGCTGCCTTTCT D hsa-let-7d hsa-let-7d t0004262 320 767 5p AGAGGTAGTAGGTTGCATAGTT AGAGGTAGTAGGTTGCATAGTT S First, I wanna know what is the header of columns? (files do not have any header line) Second, I would like to calculate expression values for miRNAs, how can I do it? Thanks PS. I am new in miRNAseq files.

11-11-2015, 09:15 AM	#2
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,080	For ref Cross-posted: https://www.biostars.org/p/165320/ I am thinking that it is some sort of alignment format but the exact name is eluding me (and my google-fu for now). Hopefully some one else will be able to recollect. Where exactly did you get that data file from on SRA? Last edited by GenoMax; 11-11-2015 at 09:21 AM.