BOL: All site questions

How to check if fragmented set of assembly is alright ?

Shruti Paniwala — Thu, 29 Jun 2017 10:20:00 -0500

I assembled the genome, by fragmenting(split) the read data in TWO set. After assembling both sets, I am just wondering what to do the next? How to validate? Is that everything is going alright?

I only use QUAST and it seems OK to me. Any other suggestions?

Note: I assembled the genome with MIRA

What is Bioinformatics ?

BioHack — Sun, 18 Jun 2017 08:01:57 -0500

I am a computer science studentm and it might be a stupid question, but am curious to know about it. Please help be to understand this properly.

How to resolve this public key issue in Ubuntu?

Neel — Fri, 16 Jun 2017 05:01:47 -0500

Hit:12 http://download.opensuse.org/repositories/isv:/ownCloud:/desktop/Ubuntu_16.10 Packages
Fetched 1.496 B in 0s (3.442 B/s)
Reading package lists... Done
W: GPG error: http://download.opensuse.org/repositories/isv:/ownCloud:/desktop/Ubuntu_16.10 Release: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY 4ABE1AC7557BEFF9
W: The repository 'http://download.opensuse.org/repositories/isv:/ownCloud:/desktop/Ubuntu_16.10 Release' is not signed.
N: Data from such a repository can't be authenticated and is therefore potentially dangerous to use.
N: See apt-secure(8) manpage for repository creation and user configuration details.

How to create Python standalone application?

Neel — Sat, 03 Jun 2017 03:11:45 -0500

I found it hard to make a standalone application using Python. Can you pleqse suggest me a easy zay out?

How to redirect MIRA temporary file to non-NFS mounted location ?

Priya Singh — Wed, 10 May 2017 08:50:13 -0500

I run MIRA on my dataset and got the following error. I have /tmp directory mounted on non-NFS protocol. I wanted to use it for temporary location. How to do that? Sorry, M new to MIRA.

WARNING WARNING WARNING!
It looks like the directory MIRA uses for temporary files
/home/user/MIRA/mira_4.0.2_linux-gnu_x86_64_static//Test_Asbly_d_tmp_MJYclL
is on a NFS (Network File System) mount. This will slow down MIRA *considerably*
... by about a factor of 10!
If you don't want that, you have three possibilities:
1) RECOMMENDED! Use -DI:trt to redirect the tmp directory somewhere else on a
local disk or even SSD.
2) ALSO POSSIBLE: put the whole project somewhere else on your file system.
3) ABSOLUTELY NOT RECOMMENDED AT ALL: use "-NW:cnfs=warn" to tell MIRA not
to stop when it finds the tmp directory on NFS.
If you do not know what NFS is and which directory to use in "-DI:trt", ask
your local system administrator to guide you.

How to remove duplicates reads Ids ?

Abhimanyu Singh — Wed, 03 May 2017 08:41:11 -0500

I mapped reads with

bwa mem -M -t 40 allCombinedFinalSet.fa Seq.R1.fastq Seq.R2.fastq > aln.sam

Extracted the mapped reads

samtools view -f 0x2 -b aln.bam > output.bam

Extracted the fastq

bamToFastq -i output.bam -fq R1.fq -fq2 R2.fq 

grep @HISEQ578:1035:HJ2KCBCXX:1:1104:14672:39678/1 R1.fq             []
@HISEQ578:1035:HJ2KCBCXX:1:1104:14672:39678/1
@HISEQ578:1035:HJ2KCBCXX:1:1104:14672:39678/1
@HISEQ578:1035:HJ2KCBCXX:1:1104:14672:39678/1

I notice it has duplicated ....

I think this because read was mapped twice (i.e. BWAmem).

I tried fastuniq but it does not remove the duplicated reads.

Can you please help me to remove duplicated reads from fastq files.

How to run fastuniq?

Bulbul — Tue, 02 May 2017 05:34:38 -0500

I wanted to remove the duplicates from fastq file. I planned to use fastuniq but it does not have good tutorial. Can you please tell me how to use it?

http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0052249

How to resolve following error in MIRA?

Bulbul — Tue, 25 Apr 2017 09:03:46 -0500

Looking for files named in data ...Pushing back filename: "clean_a2017.R1.fq"
Could not determine filetype from data 'clean_Avaga2017.R1.fq' ("clean_a2017.R1.fq")
Pushing back filename: "clean_a2017.R2.fq"
Could not determine filetype from data 'clean_a2017.R2.fq' ("clean_a2017.R2.fq")

Fatal error (may be due to problems of the input data or parameters):

********************************************************************************
* Some 'data' entries named in the manifest file could not be verified, see *
* the log above. *
* Maybe some files are missing, not readable or there is a typo in the *
* manifest file? *
********************************************************************************

Is this right to say genome size with their contigs file size?

Marysia — Fri, 21 Apr 2017 05:24:45 -0500

I usually report and estimate the genome size by looking into file size of the contigs. Is this right way?

CGAT installation error ??

Surabhi Chaudhary — Thu, 16 Mar 2017 07:03:02 -0500