User: cpak1981

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cpak1981100
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Posts by cpak1981

<prev • 27 results • page 1 of 3 • next >
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Comment: C: DESEQ2 results - write to TSV file
... Thanks! - I looked through the manual but not the vignette - the solution is trivial ...
written 9 months ago by cpak1981100
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DESEQ2 results - write to TSV file
... How can I write the values of `Formal class 'DESeqResults' [package "DESeq2"] with 6 slots` ``` log2 fold change (MAP): condition treat vs ctrl Wald test p-value: condition treat vs ctrl DataFrame with 15729 rows and 6 columns baseMean log2FoldChange lfcSE stat ...
deseq2 written 9 months ago by cpak1981100
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Comment: C: Splitting paired-end RNA-seq data in bedgraph format according to strand
... Could you show the first 5 rows of your bedgraph-formatted files? ...
written 11 months ago by cpak1981100
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Comment: C: Stringtie prepDE.py Error line 32
... What is the full path to `/SH-11/SH-11.gtf`? ...
written 12 months ago by cpak1981100
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Comment: C: HiSAT2 segfault after long run
... @OP I believe `STAR` is less memory-hungry than `HISAT`. Could try with `STAR`? ...
written 15 months ago by cpak1981100
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Comment: C: extracting mapped reads from the bam file
... To most of us, there is no difference in what you've done and what you're asking for, so clarification is required. Please elaborate on what the difference is between what you've done and what you're asking for by editing your original post. ...
written 15 months ago by cpak1981100
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Comment: C: extracting mapped reads from the bam file
... Perhaps you're unaware of how to acknowledge answers. There should be a check mark (in addition to up/down arrows) that you as the OP can toggle on/off. ...
written 15 months ago by cpak1981100
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drosophila reference genome - flybase >6 - explanation of files
... I'm looking to download *the* latest [D. melanogaster reference genome](ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r6.18_FB2017_05/fasta/). In the link, I see, `dmel-all-chromosome-r6.18.fasta.gz`, which is what I think I want. But I also see `dmel-all-aligned-r6.18.fasta.gz` and I ...
drosophila reference genome written 16 months ago by cpak1981100
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BED columns used by MACS2
... Does anyone know which bed columns are required for MACS2? Is `chr start end name score strand` sufficient? (I'm guessing that MACS2 only requires `chr start end strand` but requires `strand` in the 6th position.) Would be great to receive confirmation about this or hear if this worked for anyone ...
bed macs2 written 17 months ago by cpak1981100
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Comment: C: good CIGAR value but poor MAPQ value
... Great, thank you for the help! ...
written 17 months ago by cpak1981100

Latest awards to cpak1981

Popular Question 7 months ago, created a question with more than 1,000 views. For stringtie (.gtf) vs ballgown (t_data.ctab) FPKM values do not match - why?
Popular Question 15 months ago, created a question with more than 1,000 views. For HISAT2 rna-strandness option

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