User: hosheaa

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hosheaa20
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3 months, 1 week ago
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Posts by hosheaa

<prev • 5 results • page 1 of 1 • next >
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Answer: A: Removing 5' Adapters from Reads
... Thanks, Jennifer. I think this would be a helpful tool to have available for everyone who are not able to have their own Galaxy. But to the point at hand, I solved the problem. First, I used "manipulate fastq" to reverse complement the entire fastq file. Then, I used Trim Galore! on the reverse com ...
written 3 months ago by hosheaa20
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Answer: A: Bowtie with -a --best --strata does not seem to limit alignments to the best str
... Thanks Jennifer. I wanted to use bowtie instead of bowtie2 because the documentation states that bowtie is still better for reads averaging less than 50. And the average length of my reads are about 30 or less (miRNA analysis). So, based on your experience, would you still recommend bowtie2 in this ...
written 3 months ago by hosheaa20
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Bowtie with -a --best --strata does not seem to limit alignments to the best strata
... I am using bowtie for illumina on the NGS Galaxy public server. This is the code for the run that I copied directly from the output SAM file: "bowtie -q -p 6 -S -v 2 -n 2 -e 70 -l 28 --maxbts 800 -a --best --strata --phred33-quals /galaxy/data/hg19/hg19full/bowtie_index/hg19full /galaxy-repl/m ...
bam galaxy bowtie alignment rna-seq written 3 months ago by hosheaa20
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Removing 5' Adapters from Reads
... Is there a way to remove 5' adapters using Trim Galore? I know that cutadapt has this capability, but does Trim Galore have this capability too? If not, any suggestion using the public Galaxy server how this could be done? Thanks ...
rna-seq written 3 months ago by hosheaa20
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FeatureCount output does not match view in IGV browser
... I have a BAM file that I view locally in IGV browser. Specifically, I am focused on hsa-mir-122. The viewer shows a count of approximately 2591 for this miRNA in my sample. However, when I use featureCounts tool in Galaxy, it only counts approximately 30. I am not seeing this behaviour with other mi ...
galaxy alignment rna-seq written 4 months ago by hosheaa20 • updated 4 months ago by Jennifer Hillman Jackson23k

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