User: jolin0701-dy

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jolin0701-dy70
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Posts by jolin0701-dy

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Comment: C: STAR installation make error
... some errors during sudo apt-get install libz-dev $ sudo apt-get install libz-dev Reading package lists... Done Building dependency tree Reading state information... Done Note, selecting 'zlib1g-dev' instead of 'libz-dev' The following NEW packa ...
written 21 months ago by jolin0701-dy70
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Comment: C: STAR installation make error
... Thanks for your reply. I prefer to install it from scratch, since I use linux cluster.... ...
written 21 months ago by jolin0701-dy70
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STAR installation make error
... I'd like to install STAR in our cluster. I download the .tar.gz files and tar -xvf this file. $cd source $make STAR Makefile:71: Depend.list: No such file or directory make: Warning: File `parametersDefault.xxd' has modification time 9.5e+03 s in the future make -C htslib lib-s ...
software error written 21 months ago by jolin0701-dy70 • updated 21 months ago by Pierre Lindenbaum118k
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(Closed) R install error
... I'd like to install R into our cluster. So I download R-3.1.1.tar.gz And then do tar zxvf R-3.1.1.tar.gz Then I'd like to use the absolute path to start R and then I got an error like this: $ /home/oasis/gordon-data/NGS-ann-project/apps/bin/R /home/oasis/gordon-data/NGS-ann-project/apps/R-3.1. ...
R written 2.1 years ago by jolin0701-dy70
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ballgown error: Rows of pData did not seem to be in the same order as the columns of the expression data.
... I'm using ballgown to analyze the data and got an error. > pheno_data <- read.table(pheno_data_file, sep="\t", header=T) > pheno_data Samples Group Sample_male_1 Group1 Sample_male_2 Group1 Sample_male_3 Group1 Sample_female_1 Group2 Sample_female_2 Group2 Sample_female_3 Group2 ...
R rna-seq written 2.2 years ago by jolin0701-dy70 • updated 20 months ago by 58483973310
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Error at GBitVec: index 7 out of bounds (size 7)
... I am following the hisat2-stringtie-ballgown pipeline in Nature protocol. I am using the example data from this paper. But when I run stringtie after stringtie-merge, I got an error. my string tie version is 1.3.1 The error is that "Error at GBitVec: index 7 out of bounds (size 7)". Any help wo ...
rna-seq written 2.2 years ago by jolin0701-dy70
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Comment: C: Error for hisat2 index for human genome
... Thanks for your answers. Should I use --large-index for hisat2-build? In the manual, it is said that hisat2-build can generate either small or large indexes. The wrapper will decide which based on the length of the input genome. If the reference does not exceed 4 billion characters but a large in ...
written 2.3 years ago by jolin0701-dy70
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Error for hisat2 index for human genome
... I'd like to build hisat2 index for human genome. Here is my command: $extract_exons.py human.gtf > human.exon $extract_splice_sites.py human.gtf > human.ss $hisat2-build -p 4 human.fa --ss human.ss --exon human.exon human_tran After quite a long time, it finished. Her ...
rna-seq written 2.3 years ago by jolin0701-dy70 • updated 2.3 years ago by Macspider2.8k
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Comment: C: how to take the subset of fastq reads in one specific chromosome
... Thanks. How to format the bam to fastq? especially for paired ends? ...
written 2.3 years ago by jolin0701-dy70
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Comment: C: how to take the subset of fastq reads in one specific chromosome
... Thanks. I know it can be used for single ends. $samtools view in.bam | awk '{printf "@%s\n%s\n+\n%s\n", $1,$10,$11}' > single.fastq But how to do it with paired ends? Thanks ...
written 2.3 years ago by jolin0701-dy70

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Popular Question 2.1 years ago, created a question with more than 1,000 views. For How to analyze RIP-seq data

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