User: star

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star120
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Posts by star

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Comment: C: bedtools intersect error?
... Thanks for your help, I can fix it with your help. This time I can do intersect for some data without any error but for some one I get `Error: Sorted input specified, but the file /path/sorted_a.bed has the following out of order record chr10 1000824 1003242 sun_2016` ...
written 21 hours ago by star120
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Comment: C: bedtools intersect error?
... Yes, unfortunately, I have an Excel file that I think it changed all things ...
written 22 hours ago by star120
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Comment: C: bedtools intersect error?
... Thanks. I done it and there are some informal data in one of my files. chr2 242335250 chr22 9-Jan 42462950 chr5 15-Feb 132225350 chr7 20-Mar 35932850 chr7 23-Feb 35917850 How can i ignore them? ...
written 23 hours ago by star120
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Merge the same coordinate in a table?
... I like to know is there any way to merge the same coordinate in a table. Table: chr1 155944562 155945214 fantom_neuron GSM1554667 9.84447 chr1 155944562 155945214 fantom_neuron GSM1554672 7.43630 chr1 155944562 155945214 fantom_neuron GSM1554678 32.77627 chr1 155945743 155946 ...
bedtools merge intersect genomics written 23 hours ago by star120 • updated 22 hours ago by zx87546.6k
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Comment: C: bedtools intersect error?
... Thanks @finswimmer, i did it but still there is the same ERROR. ...
written 1 day ago by star120
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Comment: C: bedtools intersect error?
... Thanks it worked. but I get this error `***** ERROR: too many digits/characters for integer conversion in string . Exiting...` ...
written 1 day ago by star120
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Comment: C: bedtools intersect error?
... Thanks for your reply, I updated my post. but I do not have position 10966144. A.narrowpeak is contain 12999 peak number and a.csv is contain 1555091 position. ...
written 1 day ago by star120
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bedtools intersect error?
... I like to do intersect between two file using `bedtools intersect`. first file is the output of MACS2 (narrowpeak) that I changed it to bed format using cat A.narrowPeak | sort -k1,1 -k2,2n | cut -f 1-4,7,9 | sed -n '/^[0-9,X]/Ip' | sed 's/^/chr/' > A.bed and the second file is a CSV format ...
bedtools intersect chip-seq written 1 day ago by star120
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Comment: C: ATAC-seq peak calling?
... Thank. But I like to know which file based on ENDCOD: - tagAlign file ${FINAL_TA_FILE} - BEDPE file (with read pairs on each line) ${FINAL_BEDPE_FILE} - Subsampled tagAlign file for CC analysis ${SUBSAMPLED_TA_FILE} should be used as input of the MACS2. ...
written 2 days ago by star120
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(Closed) ATAC-seq peak calling?
... I have some PE ATAC-seq data and i like to do peak calling using MACS2. I found that If I like use BAM file I have to use `-f BAMPE` option otherwise I have to change BAM file to BED and then use ` -f BED -- nomodel --shift -100 --extsize 200 `. Also, I found in ENDCODE `https://docs.google.com/do ...
macs2 chip-seq written 2 days ago by star120

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