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User: salamandra

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salamandra • 110
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Posts by salamandra

<prev • 93 results • page 1 of 10 • next >
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Beedtools intersect: more peaks intersected than intersected portions of those peaks?
... When finding the number of peaks/genomic regions in A that intersects with B and C (note even the non-overlaping part of each peak is reported): bedtools intersect -f 0.5 -r -wa -a $A -b $B -sorted | sort -k1,1 -k2,2n | uniq > Apeaks.intersectingwith.B bedtools intersect -f 0.5 -r -wa ...
beedtools intersect chip-seq rna-seq sequencing written 6 weeks ago by salamandra • 110
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Comment: C: Why command gives the error: extra operand 23243?
... It works your way, but I would like to know how can we then store the value of cat FOS_3TF_day2/anngene_FOS_3TF_day2 | tail -n+2 | cut -f12 | sort -u in a temporary variable and of cat FOS_3TF_day20/anngene_FOS_3TF_day20 | tail -n+2 | cut -f12 | sort -u in another, so that we could use ...
written 6 weeks ago by salamandra • 110
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Comment: C: Why command gives the error: extra operand 23243?
... echo $gene1 | head 100033819 100500862 10381 105375972 10579 23243 2495 283120 3012 3043 3320 378938 4811 619552 6235 647121 79007 8328 8358 9147 echo $gene2 | head 10 100 1000 10000 100008586 100009613 100009667 100009676 10001 10002 10003 100033417 100033450 100033460 100033805 10003 ...
written 6 weeks ago by salamandra • 110
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Comment: C: Why command gives the error: extra operand 23243?
... it printed both with echo. I'm not understanding what you mean ...
written 6 weeks ago by salamandra • 110
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Why command gives the error: extra operand 23243?
... Why does following command: gene1=$(cat FOS_3TF_day2/anngene_FOS_3TF_day2 | tail -n+2 | cut -f12 | sort -u) gene2=$(cat FOS_3TF_day20/anngene_FOS_3TF_day20 | tail -n+2 | cut -f12 | sort -u) comm -12 $gene1 $gene2 > common.gene.FOS3TFD2.FOS3TFD20 give the error: comm: extra oper ...
commandline comm bash written 6 weeks ago by salamandra • 110
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Comment: C: Deeptools - ComputeMatrix: Why does 'referencePoint center' gives the same heatm
... i feel a bit silly, they're actually a bit different... but still don't understand why in the peak center heatmap the darker areas are not aligned among different regions. They should be right? https://imgur.com/a/5sPUa ...
written 7 weeks ago by salamandra • 110
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Deeptools - ComputeMatrix: Why does 'referencePoint center' gives the same heatmap as 'referencePoint TSS'
... Why am getting exakly the same heatmap when using as reference Point the center of the peak or the TSS of the peak with 'Deeptools ComputeMatrix'? With 'center': computeMatrix reference-point -S file_4heatmap.bw -R file_peaks_sorted_clip.bed -out file_matrixcenter.gz --referencePoint center - ...
deeptools chip-seq sequencing written 7 weeks ago by salamandra • 110
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ChIP-seq heatmap: Which MACS2 output file should we give as input into deeptools computeMatrix?
... Hi, I want to generate an heatmap with peak intensity values for genomic regions. I'm using the 'computeMatrix' followed by 'plotHeatmap' from 'deeptools'. MACS2 outputs 3 bedGraph files: 'treat_pileup.bdg', 'control_lambda.bdg' and 'qvalue.bdg', all them i converted to bigWig. Which of those bigW ...
deeptools macs2 chip-seq computematrix rna-seq written 7 weeks ago by salamandra • 110
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Comment: C: Files to compare ChIP vs Input on genome browser: after alignment or peak callin
... also, do we still have to remove duplicates when using bamCompare? ...
written 8 weeks ago by salamandra • 110
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Comment: C: Files to compare ChIP vs Input on genome browser: after alignment or peak callin
... but still in that case, bamCompare doesn't select significant peaks, i'd still have to select those significant peaks based on macs2 peak.bed file, as sugested by Satyajeet? ...
written 8 weeks ago by salamandra • 110

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Popular Question 7 weeks ago, created a question with more than 1,000 views. For Remove/Identify deprecated IDs from a list of Entrez IDs programatically
Popular Question 9 weeks ago, created a question with more than 1,000 views. For Remove/Identify deprecated IDs from a list of Entrez IDs programatically
Popular Question 4 months ago, created a question with more than 1,000 views. For Error: Encountered internal Bowtie 2 exception (#1) (ERR): bowtie2-align exited with value 1
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