User: eem0306

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eem03060
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Posts by eem0306

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Comment: C: List of NCBI database names for standalone BLAST remote search
... Is there any way to find other NCBI database lists like prokaryotic refseq genomes? I tried to find "blastdb.txt" file in NCBI ftp but I couldn't. How did you know the name of specific database? ...
written 3.1 years ago by eem03060
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Error with MuTect: SAM/BAM file SAMFileReader is malformed
... I tried to run MuTect with following command line; /usr/lib/jvm/java-1.6.0/bin/java -Xmx2g -jar /home/exman/muTect-1.1.4.jar  --analysis_type MuTect  --reference_sequence /data/eem0306/ref/1.fa  --cosmic /data/eem0306/ref/b37_cosmic_v54_120711.vcf  --dbsnp /data/eem0306/ref/dbsnp_138.hg19.nochr.vcf ...
software error samfilereader mutect written 4.7 years ago by eem03060 • updated 4.7 years ago by Devon Ryan92k
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Comment: C: samtools sort -n error
... Oh~!! I get it ~!! thank you very much ...
written 4.7 years ago by eem03060
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Comment: A: samtools sort -n error
... Anyway, I sorted the bam file and then make fastq file using this sorted bamfile. consequently, I got 2 fastq files such as N80.result.sorted.h.qsort.end1.fq, and N80.result.sorted.h.qsort.end2.fq -rw-r--r--. 1 eem0306 users      3153 Jan 20 13:47 Makefile -rw-r--r--. 1 eem0306 users 242405917 Ja ...
written 4.7 years ago by eem03060
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Comment: A: samtools sort -n error
... OK.. I'll keep going anyway! Thanks always~!! :) ...
written 4.7 years ago by eem03060
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samtools sort -n error
... I tried to convert 'strelka result file(I already convert strelka.result.file.sam to .bam)' to fastq file. But, before doing this, I had to sort 'strelka.result.file.bam'. So I did, @samtools sort -n N20.result.sorted.h.bam N20.result.sorted.h.bam.qsort and then, I got this message [bam_trans ...
software error written 4.7 years ago by eem03060
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Comment: C: trouble with installing DiffBind R package
... OK!! I Will try!!  Thx So much! ...
written 4.9 years ago by eem03060
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Comment: C: trouble with installing DiffBind R package
... I tried to install all of zlib... and it showed a list of installed zlib like this     Setting up Install Process Package zlib-devel-1.2.3-29.el6.x86_64 already installed and latest version Package jzlib-javadoc-1.0.7-7.5.el6.x86_64 already installed and latest version Package zlib-1.2.3-29.el6. ...
written 4.9 years ago by eem03060
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Comment: C: trouble with installing DiffBind R package
... you mean  zlibbioc ?? ...
written 4.9 years ago by eem03060
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trouble with installing DiffBind R package
... I try to install "R package; DiffBind" I think other depends package was installed well..  but I got a problem like this; (I tried to do this in a various versions of R, such as R 3.1.1 or R 2.15.0)   ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** buil ...
software error R chip-seq written 4.9 years ago by eem03060

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Popular Question 3.8 years ago, created a question with more than 1,000 views. For trouble with installing DiffBind R package

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