User: RPuni

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RPuni0
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Posts by RPuni

<prev • 9 results • page 1 of 1 • next >
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Comment: C: >99% unmapped reads
... Yes, I do know too short == did not map. I am on the same organism (*D. melanogaster* reads against *D melanogaster* reference genome). I saw the quality of trimmed reads is high,what should I also check? ...
written 7 days ago by RPuni0
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Comment: C: >99% unmapped reads
... 1/3 of the reads length is 143. The lengths range from 50 to 143. ...
written 10 days ago by RPuni0
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>99% unmapped reads
... Hi everyone, I am using `STAR` to map trimmed pair-end reads of *D. melanogaster* to its reference genome downloaded from NCBI. Also gff annotations file was downloaded there. From `log.final.out` file 99.9% of reads were unmapped classified as "too short". I attach command lines used to index and ...
star rna-seq written 10 days ago by RPuni0 • updated 9 days ago by swbarnes26.0k
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Comment: C: Gene symbols of different species
... Yes, sorry, I edit the post. ...
written 19 days ago by RPuni0
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Comment: C: Gene symbols of different species
... Thank you for answering. Unluckely Flybase also uses different orthologs gene symbols with respect to the NCBI. ...
written 19 days ago by RPuni0
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Gene symbols of different species
... Hi everyone, I used `HTSeq-count` to count mapped reads to genes giving in input the `bam` file get from `STAR` and the `gff` annotation file downloaded from NCBI (used also for indexing the genome, also downloaded from NCBI). I want to find differentially expressed genes in different species of * ...
gene symbols ncbi rna-seq written 19 days ago by RPuni0
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Comment: C: Count mapped reads to genes reference
... Many thanks for your answer and your warnings. I will proceed using genome instead of the small set. ...
written 24 days ago by RPuni0
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Comment: C: Count mapped reads to genes reference
... Hi, many thanks for answering and clarifying the problems of this approach. I accept your suggestion and I will use the whole genome for mapping and one of the softwares, probably STAR, you suggested, since I didn't consider points 3 and 4 while planning. ...
written 25 days ago by RPuni0
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Count mapped reads to genes reference
... Hello everyone, I want to explore differential expression of a relatively small set of genes (~30). I used this set as reference to map reads. I used Bowtie2 to build an index of these genes sequences, then I mapped transcriptomes reads to this reference, and I got the sam files. In the sam file, ...
bowtie2 samtools rna-seq written 25 days ago by RPuni0 • updated 25 days ago by i.sudbery5.0k

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