User: Illinu

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Illinu90
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Posts by Illinu

<prev • 33 results • page 1 of 4 • next >
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obtaining unique peaks in DiffBind
... Hi, I am using DiffBind for ChIP-Seq differential binding analysis. I want to use the occupancy analysis to extract peaks that are unique to one group and are absent in the other. I run the following command and I understand that the analysis outputs peaks that are present in at least 70% of the s ...
diffbind chip-seq differential written 2 days ago by Illinu90 • updated 1 day ago by igor6.4k
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Comment: C: too many adj pvalues = 1
... Hi Devon, It just seems weird that the test finds insignificant Gene A between T and C for genotype B, when it goes from 2000 to 8000 counts with small error bars. To me there is a clear induction of this gene by the treatment compared to genotype 1. But the test considers this difference as not si ...
written 14 months ago by Illinu90
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too many adj pvalues = 1
... Hi, While analyzing a set of DEGs resulting from DESeq2, I noticed for some genes that were I 'see' differences they are not significant, but then another gene with similar behaviour, the difference is significant. They both come from different comparisons, the former with 6 replicates and the late ...
p-value deseq2 rna-seq written 14 months ago by Illinu90 • updated 14 months ago by Devon Ryan81k
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Answer: A: emtpy bcf file
... This was corrected at the mpileup step with -A option samtools mpileup -ug -A -f thal.fasta $bname-thal.nodup.sorted.bam > $bname-thal.bcf -A, --count-orphans Do not skip anomalous read pairs in variant calling. Maybe this is because the sequences I used as reference are short and the p ...
written 17 months ago by Illinu90
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Comment: C: emtpy bcf file
... Thanks @Pierre, I normally run the pipeline for some commands, some of those intermediate files I need for other tasks. But in the script above I am testing this way to see at what step it fails. So far up to the *.nodup.sorted.bam it works well, that's how I know that it is the bcf file that is not ...
written 17 months ago by Illinu90
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Comment: C: comparing three genomes?
... and what is the difference for you? It still consists of fasta files with sequences right? The question is how do you do it for three sets of 'genes' (if you want) instead of two. The problem is that what you propose doesn't work when the gene names are not the same, and when there is gene expansion ...
written 17 months ago by Illinu90
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emtpy bcf file
... I am aligning genomic reads to a set of 6 genes all saved in one file in fasta format. The sam and bam files look ok but the mpileup step returns empty bcf files, with only the header until: #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample1-thal.nodup.sorted.bam Th ...
alignment samtools mpileup written 17 months ago by Illinu90
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Comment: C: Venndiagram Using R
... Hi Ly, but with this method you cannot see up and down regulated genes right? You just plot significantly differentially expressed ...
written 17 months ago by Illinu90
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Comment: C: comparing three genomes?
... I don't see this for a set of three transcriptomes, it only presents option for comparing two nucleotide databases, can you explain how you do this if you have three databases? Thank you ...
written 17 months ago by Illinu90
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Comment: C: vcf-consensus Error: Fasta sequence does not match REF
... Hi microfuge, I am getting the same error and I mapping reads from several genotypes to one heterozygous reference and was hoping to get the consensus files for each genotype. Does this error mean it is not possible to get the consensus for each genotype individually? ...
written 19 months ago by Illinu90

Latest awards to Illinu

Great Question 14 months ago, created a question with more than 5,000 views. For Python: count how many lines have a specific word
Popular Question 14 months ago, created a question with more than 1,000 views. For Python: count how many lines have a specific word
Epic Question 2.1 years ago, created a question with more than 10,000 views. For filter out multiple rows based on values in columns - perl and R attempt
Great Question 3.1 years ago, created a question with more than 5,000 views. For filter out multiple rows based on values in columns - perl and R attempt
Popular Question 3.1 years ago, created a question with more than 1,000 views. For Python: count how many lines have a specific word
Popular Question 3.1 years ago, created a question with more than 1,000 views. For filter out multiple rows based on values in columns - perl and R attempt

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