User: sunkissbean

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Posts by sunkissbean

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Answer: A: Count intervals of non-uniquely mapped reads overlapping the genome
... Update: I tried RSEM on the cloud but somehow running the RSEM but always got an error message reading "tool error". I feel that the error probably came from when I prepared the reference as the reference file that I generated was very small (<1 MB). Specifically, I used the "RSEM prepare referen ...
written 3.4 years ago by sunkissbean0
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Answer: A: Count intervals of non-uniquely mapped reads overlapping the genome
... Thank you all for your suggestions and advices! The link really shows the importance of dealing with the multi-mappers for accurate quantification of small RNA seq. I wonder whether I can use RSEM or eXpress, both of which can be found in the tool shed and seem to give more accurate quantification o ...
written 3.4 years ago by sunkissbean0
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Answer: A: Count intervals of non-uniquely mapped reads overlapping the genome
... Thank you for your reply, Jen! Mine is 50-bp single-end sequences from small RNAs rather than RNA-seq. I mapped my sequences to mm9 using BWA and more than 80% of the reads can be mapped to the genome while the non-mappers cannot be mapped to the genome using Tophat2. The reason why I didn't use the ...
written 3.4 years ago by sunkissbean0
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Count intervals of non-uniquely mapped reads overlapping the genome
... Hello everyone, I have some SAM/BAM files containing the alignments of small RNA-seq reads to mm9 that are created by BWA. I'm interested in calculating where they are mapped to in the genome. I noticed that there are a lot of reads that are mapped to multiple loci (multi-mappers) in genome. Theref ...
bam galaxy bed written 3.4 years ago by sunkissbean0

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