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Old 02-26-2015, 12:24 AM   #21
rozitaa
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Quote:
Originally Posted by dpryan View Post
Good catch! I share your wonderment that any were concordant. I'm also surprised it didn't throw an error that the files were of different lengths.
I might have caught up the problem when I align it with only single end reads (readI). These are RNA-seq data that I am trying to map against genome reference. with bowtie I cannot get the splice junctions! So for getting the inner distance by this way I should align my RNA-seq reads against a transcriptomic reference (this mentioned before also).
Anyway now I almost have my inner size and I am trying to align them by TopHat. I will update this thread by the result of my TopHat aligning.

Thanks all!
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Old 02-26-2015, 06:00 AM   #22
rozitaa
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Thanks everyone! Now it is aligning perfectly fine with TopHat! to sum up, I got the reads inner size from aligning firstly against transcriptomics reference by bowtie and then I aligned against genomics reference by TopHat!
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align unmapped mate, insert size, rna bioanalyzer, rna-seq, rna-seq aligners

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