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Old 03-02-2011, 07:36 AM   #1
hsmart
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Default miRNAkey

Hi All,

I am referring to your publication "miRNAkey: a software for microRNA deep sequencing analysis" in Bioinformatics.

I have few questions regarding the output of the miRNAkey. Specifically I am referring to an Excel file for Differential Expression Table. For most of miRNA, there are two rows (for examples hsa-let-7a and hsa-let-7a*), what is the difference between these two miRNA? Also, it generates fold-change value of +Infinity for positive two number (for example fold-change for RPKM1=0.801 and RPKM2=591.740 is +Infinity). Is it possible to convert mapped .sam file to .bed format to visualize the data in the UCSC genome browser?

I really appreciate your help on these issues.

Thanks,

Rakesh
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Old 03-03-2011, 12:32 AM   #2
NicoBxl
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A microRNA is processed from a precursor miRNA (pre-miR). From a pre-miRNA, two miRNA are processed, the mature and the star.

So hsa-let-7a and hsa-let-7a* are processed from the same pre-miR (http://www.mirbase.org/cgi-bin/mirna...?acc=MI0000060).



To convert .sam to .bed --> http://seqanswers.com/forums/showthread.php?t=2446

For the foldchange, I don't use miRNAkey..

Nico
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Old 03-03-2011, 07:49 AM   #3
hsmart
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Hi Nico,

Thanks for your detail response. I tried to use samtools and bedtools to convert .sam files to .bed files but I used human genomes 19 as reference. But I believe it might be better to use miRBase instead. Do you have any other suggestions?

Best wishes,

Rakesh
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Old 03-28-2012, 10:11 AM   #4
gpcr
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Default miRNAkey error

Alignment summary:
Total reads: 736516
Mapped reads: 255576
Uniquely mapped reads: 249567 (97.6% of mapped reads)
Multiply mapped reads: 6009 (2.4% of mapped reads)


Error message:
.....
Use of uninitialized value in concatenation (.) or string at /downloads/miRNAkey/pipeline/make_multi_input.pl line 181, <$BWA_INPUT> line 738143.
Use of uninitialized value in concatenation (.) or string at /downloads/miRNAkey/pipeline/make_multi_input.pl line 200, <$BWA_INPUT> line 738143.
.....
Differential Expression Analysis summary:
A total of 2 different miRNAs were expressed in the two samples


its the same error at line 181 and 200 for all the samples ; and all samples show only two differentially expressed miRNAs

(i tried with Bwa.0.5.7 and 0.5.9 ): both has same errors

please do suggest me what went wrong and how to over come this error?

Last edited by gpcr; 03-28-2012 at 10:13 AM.
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