User: daniel.kim

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daniel.kim30
Reputation:
30
Status:
New User
Location:
Qiagen Sciences - Frederick Maryland
Last seen:
6 months ago
Joined:
6 months, 3 weeks ago
Email:
d*********@qiagen.com

Posts by daniel.kim

<prev • 8 results • page 1 of 1 • next >
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Comment: C: Why gene counts from RNA STAR don't match total uniquely mapped counts
... Hi Devon, This is RNAseq data not DNAseq. Using Agilent Universal Human Reference RNA that has undergone additional DNAse treatment so it can't be from DNA. ...
written 6 months ago by daniel.kim30
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(Closed) Why gene counts from RNA STAR don't match total uniquely mapped counts
... Hi, I used RNA STAR to map my reads for a stranded-RNAseq library. Within RNA STAR, i turned on the option to include gene counts and so I included an hg38 GTF file from UCSC table browser. RNA STAR said that of my 20 million total reads, 86% uniquely map (so 17 million reads uniquely mapping), h ...
galaxy alignment rna-seq written 6 months ago by daniel.kim30
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Why gene counts from RNA STAR don't match total uniquely mapped counts
... Hi, I used RNA STAR to map my reads for a stranded-RNAseq library. Within RNA STAR, i turned on the option to include gene counts and so I included an hg38 GTF file from UCSC table browser. RNA STAR said that of my 20 million total reads, 86% uniquely map (so 17 million reads uniquely mapping), h ...
galaxy alignment rna-seq written 6 months ago by daniel.kim30 • updated 6 months ago by Devon Ryan1.9k
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How do I get +/- strand orientation info from my RNAseq run?
... I made a RNAseq library using a stranded-RNAseq-library prep kit. The kit only amplifies the transcript strand. I then aligned the paired-end fastq's using HISAT2 using the option for "stranded" and FR (forward read). Typically I use featureCounts to count the genes but I now need strand orientati ...
parameters featurecounts stranded rna-seq written 6 months ago by daniel.kim30 • updated 6 months ago by Jennifer Hillman Jackson25k
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Comment: C: Which Galaxy tool can concatenate fastq files from different lanes of flow-cell?
... Thank you Jennifer! As always your answer was prompt and on the money! ...
written 6 months ago by daniel.kim30
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Which Galaxy tool can concatenate fastq files from different lanes of flow-cell?
... Which tool on Galaxy can I use to merge my fastq files from lanes 1,2,3, and 4 of a single library (paired end reads) of an Illumina NextSeq run? That way I don't have to do an alignment for each lane individually... ...
tabular galaxy concatinate fastq written 6 months ago by daniel.kim30 • updated 6 months ago by Jennifer Hillman Jackson25k
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Comment: C: How do I get ribosomal RNA counts from featureCounts of my bam files?
... Thank you Jennifer for the very helpful info and for replying back to me. I was able to use featureCounts to get my rRNA counts by getting the rRNA.gtf file from UCSC table browser and then adding that gtf file into the tool parameters. Galaxy is great and the community/forum is great! Thanks! Dani ...
written 6 months ago by daniel.kim30
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How do I get ribosomal RNA counts from featureCounts of my bam files?
... Hi, I used HISAT2 to align more RNAseq fastq files and then featureCounts to count my features. All my mRNA counts look as expected but I want to count rRNA as well, however, it is saying 0 counts for rRNA even though I did not do rRNA depletion. I really want to know my rRNA counts. I used hg19 as ...
reference de featurecounts rrna annotation written 6 months ago by daniel.kim30 • updated 6 months ago by Jennifer Hillman Jackson25k

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