User: rmf

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rmf90
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Posts by rmf

<prev • 56 results • page 1 of 6 • next >
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Answer: A: Piping Markduplicates
... How about [samblaster](https://github.com/GregoryFaust/samblaster)? ...
written 8 days ago by rmf90
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Comment: C: DGE on protein-coding and lncRNAs separately?
... DESeq2....................... ...
written 18 days ago by rmf90
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Comment: C: DGE on protein-coding and lncRNAs separately?
... Thanks for your reply. I suppose that would be reasonable if I was interested in all the annotations. Say if I was only interested in the protein-coding genes, would it still be better to use all the features? ...
written 18 days ago by rmf90
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Comment: C: DGE on protein-coding and lncRNAs separately?
... My choice of whether to run DGE on protein-coding genes/lncRNAs separately or together will change the total number of analysed features in my dataset. This will consequently change the stringency of multiple testing correction. Does this matter? My resulting DEG list based on p-values may be same i ...
written 18 days ago by rmf90
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DGE on protein-coding and lncRNAs separately?
... I carried out differential expression analyses only on protein-coding genes because that is what I was interested in. Now after a while, I am considering looking into lncRNAs as well. Should I run DGE on just the lncRNAs or combine protein-coding and lncRNAs and rerun it together? The number of ge ...
rna-seq differential gene expression written 18 days ago by rmf90 • updated 18 days ago by Nicolas Rosewick5.7k
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Comment: C: Many Differentially expressed genes but few GO terms
... Yes. by qvalue I mean, Benjamini-Hochberg adjusted p-value which I think is the same as FDR adjusted p-value. But, this is some new insight. Thanks for this. ...
written 23 days ago by rmf90
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Comment: C: bwa mem: Passing a variable to read group
... Hmmm.. Actually not. This works `echo $(sh a-illumina-read-group.sh $1)` `@RG\tID:ST-E00215_230_HJ3FMALXX_2\tSM:ST-E00215_230_HJ3FMALXX_2_ATCACG\tLB:ATCACG\tPL:ILLUMINA` This doesn't `echo <(sh a-illumina-read-group.sh $1)` `/dev/fd/62` ...
written 24 days ago by rmf90
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Comment: C: bwa mem: Passing a variable to read group
... Ahan. Yea. sure. That works. The variable prints the correct content as expected. It's just that bwa doesn't accept it. ...
written 24 days ago by rmf90
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Comment: C: bwa mem: Passing a variable to read group
... `-R echo <(sh a-illumina-read-group.sh $1) ` didn't work. Got same error. With the anti-quote, I am not sure exactly what you meant. But, I tried -R echo <(`sh a-illumina-read-group.sh $1`) and -R <(`sh a-illumina-read-group.sh $1`). Both don't work. I get the same error as before plus thi ...
written 24 days ago by rmf90
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bwa mem: Passing a variable to read group
... I would like to add read group info (`-R`) during the mapping/alignment stage as part of my variant calling gatk pipeline. I am doing something like this: bwa mem \ -M \ -t 8 \ -v 3 \ -R <(sh a-illumina-read-group.sh $1) \ "$path_dr_bwaindex_genome" \ $1 $2 where th ...
variant calling bwa-mem alignment bwa gatk written 24 days ago by rmf90 • updated 24 days ago by Pierre Lindenbaum101k

Latest awards to rmf

Popular Question 11 weeks ago, created a question with more than 1,000 views. For Design matrix not of full rank.
Popular Question 3 months ago, created a question with more than 1,000 views. For Design matrix not of full rank.
Popular Question 12 months ago, created a question with more than 1,000 views. For RNA Seq: GC Content extra peak
Student 12 months ago, asked a question with at least 3 up-votes. For Consequences of degraded DNA for Sequencing
Scholar 13 months ago, created an answer that has been accepted. For A: bowtie2-build cannot use multiple cores
Supporter 18 months ago, voted at least 25 times.

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