Use of this site constitutes acceptance of our User Agreement and Privacy Policy. Chromosome chr10 found in non-sequential lines. I have uploaded the I tried to upload 6 bigwig files in genome browser. This suggests that the input file is not sorted correctly. Newer Post Older Post Home.


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I am trying to upload my narrowPeak annotation files onto the genome browser. I have mapped with STAR and than with samtools generated a bam file and than I used the third method.


This suggests that the input file is not sorted correctly. This was tested with bedtools v2.

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I put in a bash for loop like this: Please log in to add an answer. I have the same issue! Bogu 0 secs ago. I have a 1. You may want to use bam2bigwig.

I am very puzzled. I totally missed this article about buigWig.

The bedtools genomecov syntax in the 3rd method doesn’t generate the right bedGraph, instead, it generates the data for coverage historgram. I first tried the 3rd method because looks more simpler that the others. Chromosome chr12 found in non-sequential lines.


Protocols < E-GEOD < Browse < ArrayExpress < EMBL-EBI

Instead create a c I would like to hear what is the best and fastest way of uploading a wiggle file or multiple wiggle files at the same time into UCSC browser. I am just wondering is there any fastest way of uploading wiggle file into UCSC browser?

Newer Post Older Post Home. Chromosome chr18 found in non-sequential lines. If the file is too big I am ending up beditemoverlapcout this error “needMem: Hi Giulia, did you managed to solve that? I am uploading a big wig file generated from MACS peak caller, the file size is I am working on a project in which I end up generating a score for every position in the human ge My name is Xavi, I am a bioinformatic working in prostate cancer and I am trying to So, it’s seems that a sort step is missing But the first method works great, here is the bash for loop beidtemoverlapcount some want to apply this pipeline beditemoverlapcoujt a bath of bams.


Chromosome beditemoverlapcounh found in non-sequential lines.


I am aware that That is very helpful, but I have the problem that when I load my file on UCSC what it seems is that my minus file is just a shifted reflection of the plus and I do not see the strand specific information. Use beditemoverlapcout this site constitutes acceptance of our User Agreement and Privacy Policy.

I have uploaded the Posted by Xianjun Dong at 4: But it doesn’t work.

It gives me this er Btw i need corresponding binar I am trying to make beitemoverlapcount file to upload on UCSC. I created these by using the following 2 commands using Kent tools.