Monday, September 25, 2017

fastq-dumper


transfer unknown while writing file within file system module - system I/O error

home folder is full, please clean ncbi folder.

https://www.biostars.org/p/173968/

https://edwards.sdsu.edu/research/fastq-dump/


The SRA (Sequence Read Archive) is a public repository of DNA sequence data. When you run sam-dump or fastq-dump from the sratoolkit, it will first actually use prefetch to download a “temporary” .sra file, which it then converts to either sam or fastq format. By default, sratoolkit will download .sra files to a subfolder in your home folder ($HOME/ncbi/public/sra). This is a bad thing because 1) your home folder may have a space quota, and 2) these downloaded files won’t be useful for others in the group, since they’re in your personal space. It’s better to tell sratoolkit to use a shared filesystem. The advertised way to change the default path uses a graphical interface called vdb-config -i, which is not ideal. Luckily, all this GUI does is add a setting to a config file that sratoolkit reads, so we can bypass the GUI completely and edit the config file directly. Here’s how to change your default data storage path:
echo "/repository/user/main/public/root = \"$DATA\"" > $HOME/.ncbi/user-settings.mkfg

Now, the huge .sra files will be stored in our shared, huge filesystem instead of in your home directory.

To move the .sra files to a shared folder, please go to the fastq-dump folder. Under ncbi, modify the 
default.kfg as above.






Tuesday, August 8, 2017

compile pindel in macOS



Compiling this software is so painful. Take a note of the install process:

(1) install port and gcc-47:
https://www.macports.org/install.php
http://www.ficksworkshop.com/blog/post/installing-gcc-on-mac

A thread may be useful for your reference: https://www.biostars.org/p/59235/

(2) download pindel


git clone git://github.com/genome/pindel.git


(3) download samtools

https://sourceforge.net/projects/samtools/files/samtools/1.2/

In my mac pro, only this version works!!!!!

*****DO NOT INSTALL samtools but the htslib-1.2.1

by ./configure 
make
make install

(4) ./INSTALL Full path to /samtools-1.2/htslib-1.2.1



https://www.biostars.org/p/59235/#266755

Tuesday, August 23, 2016

samtools view bam from tophat


Instead of :


samtools view -h $f "chr15:51500254-51630795"

use: 

samtools view -h $f "15:51500254-51630795"


gviz


Links:

https://blog.liang2.tw/posts/2016/01/plot-seq-depth-gviz/

https://support.bioconductor.org/p/78604/


Full parameter description for every track:

http://rpackages.ianhowson.com/bioc/Gviz/man/AlignmentsTrack.html

Monday, August 22, 2016

bam error

[bam_header_read] EOF marker is absent. The input is probably truncated.


[bam_header_read] invalid BAM binary header (this is not a BAM file).

Cufflinks outputs these warnings. But Cufflinks still generates isoform results.