User: Gary
Gary • 450
- Reputation:
- 450
- Status:
- Trusted
- Location:
- Taiwan/Taichung/China Medical University Hospital
- Last seen:
- 1 year, 5 months ago
- Joined:
- 3 years, 10 months ago
- Email:
- y**********@gmail.com
Posts by Gary
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... Hi,
Could you help me about the bowtie2 error message below that I don’t understand? I run HiC-Pro (Servant et al., 2015) for our chicken HiChIP data (Mumbach et al., 2016) with 40bp paired-end reads. HiC-Pro is an aligner based on bowtie2. After running, bowtie2 showes error message below. Could y ...
written 18 months ago by
Gary • 450
• updated
13 months ago by
ashwinkelkar • 10
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Comment:
C: htseq-count cannot find pysam
... Hi,
After google, I try to set the $PYTHON_PATH, but it doesn’t work below. Could you teach me how to set $PYTHON_PATH correctly? Many thanks.
gary > pwd
/Users/gary
gary > source ~/.bash_profile
Welcome gary, the current time is
gary > cat .bash_profile
…
export PATH=$PATH:/Users/ ...
written 21 months ago by
Gary • 450
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Comment:
C: htseq-count cannot find pysam
... Thanks a lot. My htseq-count on /usr/local/bin/htseq-count. Could you teach me how to set the $PYTHON_PATH? Thanks again. ...
written 21 months ago by
Gary • 450
0
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4.2k
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Comment:
C: htseq-count cannot find pysam
... Thanks a lot. However, it doesn't work on my MacBook Pro as the below.
gary > pwd
/Users/gary
gary > sudo pip install pysam
The directory '/Users/gary/Library/Caches/pip/http' or its parent directory is not owned by the current user and the cache has been disabled. Please check the permiss ...
written 21 months ago by
Gary • 450
0
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886
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... I will. Thanks a lot. ...
written 21 months ago by
Gary • 450
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886
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... You are right. One of my colleagues who can write codes for Matlab has helped me to install PySam on my Mac several times, but it didn’t work. It is the reason why I use sam, but not bam files to run RNA-Seq quantification by htseq-count. When I have time, I would like to deal with this issue. Do yo ...
written 21 months ago by
Gary • 450
0
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0
answers
886
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... Thanks a lot. I cannot know this problem without your help. In my previous lab, they build a local Galaxy, and use TopHat2 to run RNA-Seq alignments. These bam files were downloaded from their local Galaxy, and uploaded to a Network-attached storage (NAS) by them. Then I downloaded these bam files f ...
written 21 months ago by
Gary • 450
0
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... Because I can run samtools to convert bam to sam for other RNA-Seq samples, I think it is not an issue in my case. Please see an example detail below.
gary > pwd
/Users/gary/Downloads
gary > ll
total 4645256
-rw-r--r--@ 1 gary staff 1.0G Mar 10 10:39 ...
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... Thank you so much. I have tried your suggestions, but they don’t work on my MacBook Pro (the detail below). By the way, I don’t have cmake, and have not installed bamtools successfully. I only use htseq-count for RNA-Seq quantification, and you can see my BamToSamToHTSeq.txt file below. I convert ba ...
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... I have to correct some information. If "make" means I compile samtools by myself, I could compile samtools by myself. However, I don't remember where I downloaded samtools and how I installed it. So, it is hard to say whether I compile it or not. ...
written 21 months ago by
Gary • 450
Latest awards to Gary
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For ChIP-Seq contaminated by human tissue?
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