User: ooluwayiose

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Posts by ooluwayiose

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smallRNA-seq alignment with bowtie1:what is the argument for handling multi-mapped reads?
... Hey. I am working on smallRNA-seq data with the final goal of investigating differential expression analysis. I used bowtie1 for mapping with the following specification: `bowtie -p 10 -n 2 -m 1 -k 1 --strata --best -x index -q *fq` The summary statistics I got are as follows: #reads proces ...
bowtie1 alignment smallrna-seq multi-mapped reads written 9 days ago by ooluwayiose0 • updated 8 days ago by GenoMax96k
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Comment: C: Zero small RNA counts on both featureCounts and HTseq
... @GenoMax, thank you so much for your help. I did not know it was possible to count small RNA sorted bam files directly and easily with **samtools idxstats** without either HTseq or featurecounts. That was really helpful. Also, this may sound naive but I wonder what may be the pros and cons of usin ...
written 21 days ago by ooluwayiose0
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Comment: A: Zero small RNA counts on both featureCounts and HTseq
... @GenoMax, thanks for a prompt response. Still confused, please are you referring to a mismatch in my gtf file (columns 3 & 9) or my .bam file. Please how do I make them match in all locations? The URS* in column 3 of the bam file seems to be the RNAcentral ID and I wonder if that needs to change ...
written 21 days ago by ooluwayiose0
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Comment: A: Zero small RNA counts on both featureCounts and HTseq
... For some reason, the image icon above appeared not to work. Here are the links again: gtf: ![https://ibb.co/19sv9WV][1] mapped.sorted.bam: ![https://ibb.co/0cxmB8w][2] featureCounts output: ![https://ibb.co/hWmxq8s][3] [1]: https://i.ibb.co/sF5mFYS/gtf-file.png [2]: https://i.ibb.co/Bt9c4 ...
written 22 days ago by ooluwayiose0 • updated 22 days ago by GenoMax96k
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Comment: A: Zero small RNA counts on both featureCounts and HTseq
... Thanks GenoMax, I used imgbb as recommended in the link. Please see the links below: ![.gtf][1] ![mapped.sorted.bam][2] ![featureCounts output][3] [1]: https://ibb.co/19sv9WV [2]: https://ibb.co/0cxmB8w [3]: https://ibb.co/hWmxq8s ...
written 22 days ago by ooluwayiose0
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Comment: C: Zero small RNA counts on both featureCounts and HTseq
... The is smallRNA-seq data. My apologies about the images. here are the links to the three images now using googledrive image hoster. [.gtf][1] [mapped.sorted.bam][2] [featureCounts snapshot][3] [1]: https://drive.google.com/file/d/1N01yy2w0eBJV9Wc9MXa89aISXA7sm_yp/view?usp=sharing [2]: https ...
written 22 days ago by ooluwayiose0
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Zero small RNA counts on both featureCounts and HTseq
... Hey folks, I'm new with RNAseq analysis and would appreciate your assistance in figuring this out. I have single end reads from RNAseq data with the goal of profiling all available sncRNAs in the tissue (n = 96 samples). Post-trimming Fastqc distribution ranged between 16 - 50nt. Here are my steps: ...
alignment rna-seq sequencing written 22 days ago by ooluwayiose0

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