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Old 07-09-2014, 11:07 AM   #1
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Location: Cuba

Join Date: Aug 2013
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Default RNASeq de novo from TopHat unmapped.bam

I ran a RNASeq pipeline for human skin samples using TopHat2 and hg19 as the reference genome and, because I wanted to find contaminants from other organisms, I used the reads contained in unmapped.bam as input (after convert them to fastq files) for de novo RNASeq with Trinity.

I don't understand why some contigs generated by Trinity map with 100% identity in about 3000 bp alignment to ensembl transcripts.

Why the reads from which that contigs were generated were in unmmaped.bam file produced by TopHat?

Any idea?
demold is offline   Reply With Quote
Old 12-27-2017, 07:30 PM   #2
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Location: USA

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I read your post. I am also trying to construct a de novo assembly using unmapped.bam files from TopHat but I am getting errors. Did you sort your .bam reads before converting them to fastq? I know you did it long time ago but Can you please help me by sharing the steps?
Zunaira is offline   Reply With Quote
Old 05-11-2018, 06:07 AM   #3
Location: Lund, Sweden

Join Date: Mar 2013
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Hi Zunaira,

you haven't stated the exact problems you see, but TopHat unmapped.bam files generally contain several errors that can impede processing.

We published a software called TopHat-Recondition to fix these errors a while ago, please see the paper and the software.

Let me know in case you have questions.
offspring is offline   Reply With Quote

de novo rna-seq, tophat 2, trinity assembly, unmaped reads

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