User: dec986

gravatar for dec986
dec98630
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30
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New User
Location:
United States
Last seen:
2 days, 10 hours ago
Joined:
3 years ago
Email:
d*****@gmail.com

Posts by dec986

<prev • 78 results • page 1 of 8 • next >
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Creating genome alignment
... Hello, I am confused about the difference between `GRCh37.p13.genome.fa` (767 MB, http://www.gencodegenes.org/releases/19.html) and `GRCh37.primary_assembly.genome.fa` (830 MB http://www.gencodegenes.org/releases/27lift37.html) which is lifted from Gencode release 27. I want to use the most recent ...
star rna-seq written 4 days ago by dec98630 • updated 4 days ago by lshepard130
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Comment: C: STAR Alignment Score reduced after trimming
... great, thanks, I have to let my colleagues know. We're comparing several different RNA-Seq pipelines. ...
written 5 days ago by dec98630
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Comment: C: STAR Alignment Score reduced after trimming
... thank you! who is "our"? ...
written 5 days ago by dec98630
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STAR Alignment Score reduced after trimming
... Hello, I'm comparing three different QC tools (trimgalore, trimmomatic, & bbduk) and then seeing how STAR alignments are affected by all of them, comparing against a noQC run. Specifically, I am comparing the "AS" and "nM" fields in the BAM file. I figured that the alignment scores should inc ...
star rna-seq written 5 days ago by dec98630 • updated 5 days ago by Devon Ryan76k
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STAR => featureCounts pipeline
... Hello, I'm looking at STAR's `--quantMode TranscriptomeSAM` option, and am puzzled, should I use `TranscriptomeSAM` for input into featureCounts, or should I use the `Aligned.sortedByCoordinate.out.bam` file output by STAR for input into featureCounts? I already get the counts from `--quantMode Ge ...
rna-seq written 9 days ago by dec98630 • updated 9 days ago by h.mon11k
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Trimmomatic destroys right-hand paired-end sequences, how to avoid?
... Hello everyone, I am attempting to run trimmomatic, but am having issues: 1) how to identify necessary adapters? TrimGalore does this automatically, the only way I can think of to do this is to automatically load everything in the database, or just read TrimGalore's output, is this practical? 2) ...
trimmomatic qc written 17 days ago by dec98630 • updated 17 days ago by Martombo1.9k
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Cannot match machine name with Machine Type
... Hello, I have a fastq file that says it was run on a machine with a unique ID `NB501139` but I don't know how I can match this with a machine type, I assume this is an Illumina machine? I cannot find any Illumina instrument type that would have a name like this? I need this for trimmomatic to kno ...
trimmomatic fastq qc rna-seq written 24 days ago by dec98630 • updated 24 days ago by Devon Ryan76k
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Comment: C: stringtie cannot recognize Gencode GTF
... Hi Macspider, that's the output from stringtie, not the input. The input GTF and GFF were downloaded from Gencode. ...
written 5 weeks ago by dec98630
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Comment: C: stringtie cannot recognize Gencode GTF
... hi Macspider, I'm getting the same error with the Gencode GFF as I am with the Gencode GTF. ...
written 5 weeks ago by dec98630
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Comment: C: stringtie cannot recognize Gencode GTF
... @Macspider thanks I've updated the question ...
written 5 weeks ago by dec98630

Latest awards to dec986

Popular Question 7 weeks ago, created a question with more than 1,000 views. For Installation of Bcl2Fastq Fails
Scholar 3 months ago, created an answer that has been accepted. For A: Alignment with STAR produces unique bam files, but identical output from bedtool
Popular Question 10 months ago, created a question with more than 1,000 views. For Installation of Bcl2Fastq Fails
Popular Question 10 months ago, created a question with more than 1,000 views. For R programming: Keep Heatmap Items Within Image Frame
Popular Question 10 months ago, created a question with more than 1,000 views. For Conversion between .bedGraph or .bw to 7-column format
Popular Question 10 months ago, created a question with more than 1,000 views. For edgeR: no residual df: Cannot estimate dispersion
Supporter 10 months ago, voted at least 25 times.
Popular Question 15 months ago, created a question with more than 1,000 views. For DESeq2 comparison failure
Scholar 21 months ago, created an answer that has been accepted. For A: Alignment with STAR produces unique bam files, but identical output from bedtool

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