User: Lila M
Lila M • 460
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Posts by Lila M
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... Hi, there are no replicates, they are ChiP-seq samples in different conditions. ...
written 6 days ago by
Lila M • 460
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... Hi everybody,
I have different samples that I used to calculate the coverage over specific data set. I did it using deeptools, so my final output is something like this
s1 1,923575916 1,92340092 1,918008392 1,915392666 ...
s2 1,993446863 1,931309701 1,925363124 1,935658019 ...
s3 2,034 ...
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... Hi Kevin, Thank you for such an extensive response!
What I basically did , was to transform my bam file into a bed one, so then I was able to get the coverage by running
bedtools coverage -a file.bed -b file.bedGraph -counts > coverage_by_counts
...
written 5 weeks ago by
Lila M • 460
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... Hi, the chromosomes appeared as "chr1"
SRR6497149.3455795 16 chr1 10533 1 65M * 0 0AAGTACCACCGAAATCTGTGCAGAGGAGAACGCAGCTCCGCCCTCGCGGTGCTCTCCGGGTCTGT EGGGGFGGGGGGEGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGDGGGGGGGGFGGFGGGEBBBBB AS:i:-10 XS:i:-10 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:0G26C37 YT:Z:UU
howev ...
written 5 weeks ago by
Lila M • 460
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... Hi everybody,
I'm stuck in the middle of something. I have a selected gene list `(bed file`) like this:
chr start end strand gene geneLength
chr1 185217 195411 - ENSG00000279457 10194
chr1 725885 778626 - ENSG00000228327 52741
chr1 725885 778626 - ENSG00000228327 ...
written 5 weeks ago by
Lila M • 460
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... Sorry but I can't figure out how to do it with those programs, more help will be very handy! Thanks! ...
written 6 weeks ago by
Lila M • 460
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... Thank you for the tip, but as far as I understand, deeptools needs the bam files or bigwig files (I only have this bed file to work with). I will have a look into genomation as I never work with it before. ...
written 6 weeks ago by
Lila M • 460
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... Hi everybody,
I have an issue here, let's say I have this kind of data:
chr w_start w_end ratio_w ratio_c chr txt_start txt_end strand gene
chr1 879000 879999 0.102 0.306 chr1 879584 882440 - ENSG00000188976
chr1 879000 879999 0.102 0.306 chr1 879584 894670 - ...
written 6 weeks ago by
Lila M • 460
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... I find the silly problem, I forgot to transform the bedGraph after merging using `bedGraphToBigWig` ...
written 7 weeks ago by
Lila M • 460
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...
The file that I started with is a wig file like this:
GSM2936611_BJ.c.a_merged_coverage_strand-_scaled_bin10_EXT0.copy2_lane2_rep1.wig.gz
track type=wiggle_0 name=BJ.c.a.- description=BJ.c.a.- maxHeightPixels=50:30:11 color=150,50,110 alwaysZero=on
variableStep chrom=chr1 ...
written 7 weeks ago by
Lila M • 460
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