User: Morris_Chair

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Morris_Chair190
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Posts by Morris_Chair

<prev • 179 results • page 1 of 18 • next >
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Comment: C: ballgown and pData
... Hi Asad, I am sorry but at the end for my analysis I used a different pipeline so I don't know what to say about this error. I hope someone else will be helpful for you ...
written 23 days ago by Morris_Chair190
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Comment: C: MACS sampling down
... Hi Friederike, the rational should be to have the same amount of reads in all samples and avoid extra peaks in samples with more reads. let say that with the protein of interest I have a file of 1 million of reads, input 1.5 and histone acetylation 0.8 million I think to sample down considering th ...
written 27 days ago by Morris_Chair190
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MACS sampling down
... Hello everyone, I was watching a tutorial about how to use MACS, one step is for sampling down treatment and control in order to have the same amount of reads. Do you guys think that I should sample down everything? including input, histone acetylation and methylation as well? thank you ...
chip-seq written 27 days ago by Morris_Chair190
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Comment: C: samtools sort error
... ok probably I solved, I m doing again the alignment by using this code to get directly the bam file bwa mem ref.fa read1.fq read2.fq | samtools view -o output.bam finger crossed.. and thank you :) ...
written 28 days ago by Morris_Chair190
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Comment: C: samtools sort error
... Oh I didn't know that the usage was different, I used bwa because I read that is better for alignment of ChIP-seq experiment compared to bowtie2 but then how can I convert this sam file to bam from bwa? thank you ...
written 28 days ago by Morris_Chair190
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Comment: C: samtools sort error
... Hi Pierre, It doesn't like anything I do with samtools on this files, I don't work on my own computer but I use the workstation of the research institute. All tools are already installed there. To get the executable for samtools, I used bwa with this cmd line bwa mem hg38.fa -1 R1_001.fastq ...
written 28 days ago by Morris_Chair190
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samtools sort error
... Hello everyone, I am getting an error by sorting sam file to bam files, please attached is the screenshot ![enter image description here][1] this is the code I use samtools sort pf382wt-bcat.sam > pf382wt-bcat.bam > Failed to open file pf382wt-bcat.sam samtools view: failed to open ...
chip-seq written 28 days ago by Morris_Chair190
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bowtie mate 2 error
... Hello everyone, I'm working on ChIP-seq files and I'm getting this type of error > mem: invalid option -- '2' here is the code : bwa mem hg38.fa -1 R1_001.fastq.gz -2 R2_001.fastq.gz | samtools sort > file.bam I'm working on paired end ChIP-seq experiment so I have to use both fil ...
chip-seq written 29 days ago by Morris_Chair190 • updated 27 days ago by h.mon30k
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Comment: C: Pathways Analysis in R
... Hi Julia, you may want to use genecodis or DAVID tool for this type of analysis by selecting the more expressed and significant genes ...
written 5 weeks ago by Morris_Chair190
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Comment: C: Pubmed gene database
... probably they include also alternative spliced genes ...
written 6 weeks ago by Morris_Chair190

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