User: alim

gravatar for alim
alim10
Reputation:
10
Status:
New User
Location:
United Kingdom
Last seen:
1 year, 1 month ago
Joined:
2 years, 5 months ago
Email:
a***@mrc-lmb.cam.ac.uk

Posts by alim

<prev • 10 results • page 1 of 1 • next >
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Comment: C: DeepTools plotCorrelation Error "IOError: [Errno 22] Invalid argument"
... ah well done Devon ! Many thanks ! Would it be possible for me to try re-running multiBamSummary on Galaxy again anytime soon? ...
written 14 months ago by alim10
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Comment: C: Help with plotCorrelation tool - error message
... Hi Devon, it is Galaxy Version 2.3.5.0. What would be the best way to send you those BAM files? Many thanks for looking into it. I would really like to analyse these data before the end of the week if possible ...
written 14 months ago by alim10
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Comment: C: Help with plotCorrelation tool - error message
... Hi Devon, I just double checked and you're right, the multiBamSummary file was actually an empty file with 0 byte of data ! I should have checked before assuming it was okay and put it into plotCorrelation. There is however no error message from the multiBamSummary. When I ran mBS, my input files ...
written 14 months ago by alim10
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Comment: C: Help with plotCorrelation tool - error message
... Hi Devon, it is 0 bytes indeed. Any advice on how to get over this would be much appreciated ! ...
written 14 months ago by alim10
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DeepTools plotCorrelation Error "IOError: [Errno 22] Invalid argument"
... Dear all, I used a matrix generated from multiBamSummary to run plotCorrelation but the error message below was generated: Fatal error: Exit code 1 () Traceback (most recent call last): File "/galaxy-repl/main/jobdir/014/089/14089566/conda-env/bin/plotCorrelation", line 7, in main() Fil ...
plotcorrelation galaxy deeptools tool error written 14 months ago by alim10 • updated 14 months ago by Jennifer Hillman Jackson23k
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Comment: C: Help with using the multiBam Summary tool - error message
... Thanks so much Devon and Jen - I will recheck my data and see if it was using the correct reference genome. Cheers, Alfred ...
written 14 months ago by alim10
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Answer: A: Help with using the multiBam Summary tool - error message
... Hi Devon, Many thanks for getting back to me. What sort of range of bin size would you suggest please and how can I estimate that? My reads are all 50-bp fragments, aligned to mouse mm10 genome. ...
written 14 months ago by alim10
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Help with using the multiBam Summary tool - error message
... Hello, I have just aligned some reads using Bowtie2 and am wanting to look at correlation between my replicates using the plotCorrelation tool. However, this requires a matrix file to first be generated with the multiBamSummary tool. I tried running the latter to generate the matrix but this error ...
bam software error rna-seq written 14 months ago by alim10
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Answer: A: Installing MACS stuck at 'Cloning'
... Hi Bjoern,  Thank you very much for replying me. I have tried to uninstall and reinstall but it's the same. How would you suggest I repair it ?  I have downloaded MACS2 but the adjustable parameters are different. For example, in MACS I could control the mFOLD parameter, but this option seem to be ...
written 2.4 years ago by alim10
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Installing MACS stuck at 'Cloning'
... Dear all,  I am trying to install MACS from the Tool Shed onto my local Galaxy but it is stuck at the 'Cloning' step. Does anyone have such experience before and could advice on what to do please ?  Also, can anyone share their experience between using MACS and MACS2 please ? How comparable are th ...
macs galaxy written 2.4 years ago by alim10

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