User: Gary

gravatar for Gary
Gary450
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

<prev • 68 results • page 1 of 7 • next >
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Error message produced by bowtie2 (HiC-Pro)
... 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 ...
bowtie2 hic-pro hichip alignment written 18 months ago by Gary450 • updated 13 months ago by ashwinkelkar10
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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 Gary450
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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 Gary450
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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 Gary450
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Comment: C: Error of bam-to-sam conversion using samtools
... I will. Thanks a lot. ...
written 21 months ago by Gary450
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Comment: C: Error of bam-to-sam conversion using samtools
... 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 Gary450
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Comment: C: Error of bam-to-sam conversion using samtools
... 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 Gary450
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Comment: C: Error of bam-to-sam conversion using samtools
... 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 ...
written 21 months ago by Gary450 • updated 21 months ago by genomax59k
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Comment: C: Error of bam-to-sam conversion using samtools
... 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 ...
written 21 months ago by Gary450 • updated 21 months ago by genomax59k
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Comment: C: Error of bam-to-sam conversion using samtools
... 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 Gary450

Latest awards to Gary

Voter 21 months ago, voted more than 100 times.
Popular Question 21 months ago, created a question with more than 1,000 views. For ChIP-Seq contaminated by human tissue?
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: Network analysis software
Popular Question 2.4 years ago, created a question with more than 1,000 views. For htseq-count cannot find pysam
Popular Question 2.6 years ago, created a question with more than 1,000 views. For How to modify a gff3 file for HTSeq?
Scholar 3.5 years ago, created an answer that has been accepted. For A: 200 vs 400 bp Ion Torrent
Supporter 3.6 years ago, voted at least 25 times.
Scholar 3.7 years ago, created an answer that has been accepted. For A: 200 vs 400 bp Ion Torrent
Teacher 3.7 years ago, created an answer with at least 3 up-votes. For A: Network analysis software

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