User: lumingflank1

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Posts by lumingflank1

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change ".." to tab or change a string of characters into different column
... I want to change a CTCF CHIA-PET bed file data to its two end bed file. how can I change chrX:154145949..154146870-chrX:154314445..154315402,2 chrX:154208778..154209800-chrX:154376894..154377812,3 chrX:154208831..154209797-chrX:154285357..154286294,4 into ...
chip-seq written 5 days ago by lumingflank10 • updated 5 days ago by cpad01123.0k
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can I use homer findpeaks -style dnase to analyse Faire-seq file?
... can I use homer findpeaks -style dnase to analyse Faire-seq file? or which style is better or no style suite for Faire analysis? just in this way: findpeaks ${id%%.*}/ -i ctrl/ -style dnase > ${id%%.*}.Fairepeak.txt attached all the style in homer fin ...
chip-seq written 14 days ago by lumingflank10
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Comment: C: how to keep column 6 (normalized tag count) in peaks.txt file called by Homer ca
... why we have to clear lines with #, which didnot impact the intersect manipulation and result? even in homer's pos2bed.pl .txt >.bed, the new .bed file keeps the lines with # ...
written 20 days ago by lumingflank10
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Answer: A: error report:while running fastq-dump
... Try sudo fastq-dump SRR029687 directly ...
written 22 days ago by lumingflank10
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Comment: C: how to keep column 6 (normalized tag count) in peaks.txt file called by Homer ca
... Thank you, I use these code, and the column 6 will be kept after bedtools intersect cut -f 1,2,3,4,6 peaks.txt | awk '{print $2"\t"$3"\t"$4"\t"$1"\t"$5}' >peak1.bed pos2bed.pl peaks.txt > peak2.bed awk 'NR==FNR {h[$4] = $5; next} {print $1"\t"$2"\t"$3"\t"$4"\t"$5"\t"$6"\t"h[$4]} ...
written 4 weeks ago by lumingflank10
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Comment: C: how to keep column 6 (normalized tag count) in peaks.txt file called by Homer ca
... Thank you , I know it, however pos2bed.pl will cut the column 6 from txt file to bed file. Even when I transform bed to txt again, there is still no column 6. ...
written 4 weeks ago by lumingflank10
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how to keep column 6 (normalized tag count) in peaks.txt file called by Homer callpeaks after pos2bed manipulation?
... I use HOMER to call peaks getting peaks.txt file. Then I use pos2bed.pl to transform peaks.txt to peaks.bed However, the column 6 loss after the transform, which showed the normalized tag count (equal to RPKM reflecting peak density). ...
chip-seq written 4 weeks ago by lumingflank10 • updated 4 weeks ago by prakash100

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