Dear all,
I have generated bedgraphs that I can visualize in UCSC. For example:
I want to compare bam of samples from 2 conditions by visualizing them on UCSC. In one condition, I have 5 samples and in the other condition, there are 16 samples. I was told that it is possible to visualize only one "summarizing sample" per condition.
I ran unionBedGraphs from bedtools on the 5 samples of condition 1:
I got a merged file of 1.4Go:
When I try to upload this file in UCSC, I get the following error:
I changed the header line with:
Then, I took only the 500,000 first lines of Cond1.bedGraph with "track type=bedGraph name=Cond1" as Header, but again, I got an error:
Finally I tried another header:
ending with:
Now, I wonder if it is possible to visualize this merged file in UCSC.
Can you please tell me if it is possible to visualize it somehow? Should I modify something in the header?
Thank you for your help,
Jane
I have generated bedgraphs that I can visualize in UCSC. For example:
Code:
head BIO_31-T1-ARN.bedGraph track type=bedGraph name=BIO_31-T1-ARN chr5 170000000 170000600 0.00 chr5 170000600 170000700 2.00 chr5 170000700 170000850 0.00 chr5 170000850 170000950 2.00 chr5 170000950 170001000 0.00 chr5 170001000 170001100 2.00 chr5 170001100 170001250 0.00 chr5 170001250 170001400 2.00 chr5 170001400 170002200 0.00
I ran unionBedGraphs from bedtools on the 5 samples of condition 1:
unionBedGraphs -i BIO-12-T1-ARN/tophat_out/BIO-12-T1-ARN.bedGraph BIO_26-T1-ARN/tophat_out/BIO_26-T1-ARN.bedGraph BIO_28-T1-ARN/tophat_out/BIO_28-T1-ARN.bedGraph BIO_052_T1_ARN/tophat_out/BIO_052_T1_ARN.bedGraph BIO_057_T1_ARN/tophat_out/BIO_057_T1_ARN.bedGraph -header > Cond1.bedGraph
Code:
head Cond1.bedGraph chrom start end chr11 60000000 60008500 0 0 0 0 0.00 chr11 60008500 60008600 0 0 0 0 1.00 chr11 60008600 60009850 0 0 0 0 0.00 chr11 60009850 60010050 0 0 0 0 2.00 chr11 60010050 60010400 0 0 0 0 0.00 chr11 60010400 60010450 0 0 0 0 1.00 chr11 60010450 60016500 0 0 0 0 0.00 chr11 60016500 60016600 0 0 0 0 1.00 chr11 60016600 60047950 0 0 0 0 0.00
Error File 'Cond1.bedGraph' - Unrecognized format line 1 of file: chrom start end
track type=bedGraph name=Cond1
but I got the following error:
needMem: trying to allocate 1414098818 bytes (limit: 500000000)
but I got the following error:
needMem: trying to allocate 1414098818 bytes (limit: 500000000)
Error File 'Cond1_500000.bedGraph' - Error line 2 of custom track: Expecting + or - in strand
Code:
head Cond1_500000_v3.bedGraph chrom start end S1 S2 S3 S4 S5 chr11 60000000 60008500 0 0 0 0 0.00 chr11 60008500 60008600 0 0 0 0 1.00 chr11 60008600 60009850 0 0 0 0 0.00 chr11 60009850 60010050 0 0 0 0 2.00 chr11 60010050 60010400 0 0 0 0 0.00 chr11 60010400 60010450 0 0 0 0 1.00 chr11 60010450 60016500 0 0 0 0 0.00 chr11 60016500 60016600 0 0 0 0 1.00 chr11 60016600 60047950 0 0 0 0 0.00
Error File Cond1_500000_v3.bedGraph' - Unrecognized format line 1 of file: chrom start end S1 S2 S3 S4 S5 (note: chrom names are case sensitive, e.g.: correct: 'chr1', incorrect: 'Chr1', incorrect: '1')
Can you please tell me if it is possible to visualize it somehow? Should I modify something in the header?
Thank you for your help,
Jane