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Forum: Bioinformatics 07-09-2013, 06:41 AM
Replies: 0
Views: 1,205
Posted By gene coder
Meaning of 1KGP FASTA file headers

I downloaded the 1KGP fasta file from ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/. 1:1:249250621 means chr1:1-249250621 obviously. What does the final "1" in the header mean?
Forum: MGISEQ (FKA Complete Genomics) 03-05-2013, 03:26 AM
Replies: 0
Views: 3,540
Posted By gene coder
Are public CG reads SE reads or PE reads?

I was running head -20 on the file ftp://ftp2.completegenomics.com/YRI_trio/MAP_Build37_2.0.0/NA19240/NA19240-L2-200-37-MAP/GS27651-FS3-L01/reads_GS27651-FS3-L01_013.tsv.bz2. The output suggests that...
Forum: Genomic Resequencing 01-09-2013, 12:09 PM
Replies: 1
Views: 1,463
Posted By gene coder
Tips for writing an own aligner

I am trying to write an own special-purpose aligner for read alignment or realignment. I need some help.

Say that I have found a particular coordinate for one read of a read-pair. The mate of this...
Forum: Core Facilities 11-01-2012, 08:24 AM
Replies: 0
Views: 2,220
Posted By gene coder
Missing FASTQ files in European 1KGP trio?

I think that some FASTQ files containing exome reads from the European trio in the 1KGP project are missing.

Read groups in an exome file...
Forum: Bioinformatics 10-11-2012, 08:06 AM
Replies: 2
Views: 1,191
Posted By gene coder
Thanks. That is what I needed to know.

Thanks. That is what I needed to know.
Forum: Bioinformatics 10-11-2012, 07:32 AM
Replies: 2
Views: 1,191
Posted By gene coder
Nucleotides M and R in human reference no. 37

A, C, G and T are "normal" nucleotides and N represents unknown nucleotides in repetitive sequences or SNPs. When checking the reference genome from 1KGP...
Forum: Bioinformatics 09-06-2012, 04:49 AM
Replies: 3
Views: 1,492
Posted By gene coder
Does anybody know how to make effective text...

Does anybody know how to make effective text searches at ENA or SRA? I am looking for sequencing projects (whole-genome or exome) on the Illumina platform. The primary species in mind is humans, but...
Forum: Bioinformatics 02-10-2012, 04:23 AM
Replies: 2
Views: 1,800
Posted By gene coder
Problem solved! I have managed to find it in the...

Problem solved! I have managed to find it in the source file BLibDefinitions.h. It is also in the file bfast-book.pdf.

/* Scoring matrix defaults */
#define SCORING_MATRIX_GAP_OPEN -175
#define...
Forum: Bioinformatics 02-10-2012, 02:33 AM
Replies: 2
Views: 1,800
Posted By gene coder
BFAST scoring matrix

Hello folks,

I wonder what the default scoring matrix is in BFAST. I can only find information on instructions of how to set one, but there is no information regarding the default.
Forum: Bioinformatics 01-03-2012, 03:42 PM
Replies: 3
Views: 7,709
Posted By gene coder
Thanks. I found that SamToFastq in Picard did the...

Thanks. I found that SamToFastq in Picard did the job on a chromosome of NA12878 from the 1000 Genomes Project.

1. I separated SE reads and PE reads by library into separate BAM files using...
Forum: Bioinformatics 12-22-2011, 05:19 PM
Replies: 3
Views: 7,709
Posted By gene coder
Reverse engineering BAM files: BAM -> FASTQ

How can I possibly extract the reads from a BAM file and put them into a FASTQ file for simulation (maq simutrain, then maq simulate)?

Should I just extract col. 1, 10 and 11 from a BAM file and...
Forum: Illumina/Solexa 12-15-2011, 05:53 AM
Replies: 1
Views: 2,672
Posted By gene coder
Problem solved. I have managed to find a bug in...

Problem solved. I have managed to find a bug in the makefile and notified the author. Simply change it as follows where the old code is commented:

simNGS: $(objects)
$(CC) $(DEFINES) $(CFLAGS)...
Forum: Illumina/Solexa 12-14-2011, 03:56 PM
Replies: 1
Views: 2,672
Posted By gene coder
Compiling simNGS fails

I am trying to compile simNGS, but it fails. I get these messages found below. Obviously it is a linking problem.

Download simNGS from http://www.ebi.ac.uk/goldman-srv/simNGS/ or...
Forum: Bioinformatics 07-07-2011, 04:37 AM
Replies: 4
Views: 6,456
Posted By gene coder
If I want to use dwgsim for simulating...

If I want to use dwgsim for simulating read-pairs, can anyone explain the flags for me (http://sourceforge.net/apps/mediawiki/dnaa/index.php?title=Whole_Genome_Simulation)?

What do -e and -E mean...
Forum: Bioinformatics 07-07-2011, 12:57 AM
Replies: 1
Views: 6,280
Posted By gene coder
dwgsim to simulate Illumina reads

Hello, I want to use dwgsim to simulate Illumina reads from the 1000 Genomes Project. I am particularly interested in individual NA12878.

Does anybody know what settings are (approximately or...
Forum: Bioinformatics 07-06-2011, 07:32 AM
Replies: 4
Views: 3,339
Posted By gene coder
Truncated BAM files from 1000GP

I got this error message from SAMTOOLS:

samtools view -q 30 NA12878.chrom1.SLX.maq.SRP000032.2009_07.bam 1:532036-533055
[bam_header_read] EOF marker is absent. The input is probably truncated....
Forum: Bioinformatics 07-03-2011, 04:54 PM
Replies: 4
Views: 6,456
Posted By gene coder
Thanks everyone for your replies. I want a...

Thanks everyone for your replies.

I want a sequence error simulator that should match Illumina in the 1000 Genomes Project. That is where I am getting my data from. (Illumina-specific is not a...
Forum: Bioinformatics 07-01-2011, 05:45 AM
Replies: 4
Views: 6,456
Posted By gene coder
Simulate Illumina read-pairs

Hello,

I want to simulate read-pairs using a read-length greater than 35 (up to 75). If I run MAQ, this works:

maq simulate -N 1000 -1 35 -2 35 out.read.1.fastq out.read.2.fastq...
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