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Search: Posts Made By: haojam
Forum: Bioinformatics 03-17-2014, 02:32 AM
Replies: 11
Views: 5,437
Posted By haojam
Hi All, I have a bam file that containg only...

Hi All,

I have a bam file that containg only information for chr21.
When I run sh bam2coverage.sh

command :
sh bam2coverage.sh /path for bam file/chr21.sortedpicard.rmdup.realigned.recal.bam...
Forum: RNA Sequencing 05-23-2013, 12:22 AM
Replies: 2
Views: 3,145
Posted By haojam
Dear Hsueh-Ting Chu from Taiwan Good to know...

Dear Hsueh-Ting Chu from Taiwan

Good to know about your EBARDenovo. Does it support for transcriptome data generated from other platforms like ion torrent other than Illumina.

Rocky
Forum: De novo discovery 04-25-2012, 07:27 PM
Replies: 10
Views: 3,658
Posted By haojam
paired-end reads were obtained from GAII...

paired-end reads were obtained from GAII (Illumina Genome Analyzer Pipeline v.1.4.0)
Forum: De novo discovery 04-25-2012, 07:24 PM
Replies: 10
Views: 3,658
Posted By haojam
When I try running with -I option at BWA...

When I try running with -I option at BWA alignment and converted to sam file then to bam file error occurs.

These are the comment
SEQUENCE ALIGNMENT
$ ./bwa aln -I -t 4...
Forum: De novo discovery 03-30-2012, 11:39 PM
Replies: 10
Views: 3,658
Posted By haojam
parameter set of bwa-samtools for snp calling

Hi,
Everyone, I use bwa-samtools for human genome SNPs calling, but the SRA READS are performed using the Illumina Genome Analyzer Pipeline v.1.4.0 software suite. Should I need to run BWA alignment...
Forum: Bioinformatics 09-30-2011, 02:43 AM
Replies: 29
Views: 17,407
Posted By haojam
Hello, Does BWA support SRR.....fastq.bz2...

Hello,

Does BWA support SRR.....fastq.bz2 file for aligning with the human genome reference sequence?

Regards,
HR
Forum: Bioinformatics 09-28-2011, 10:16 PM
Replies: 29
Views: 17,407
Posted By haojam
Hello, Before indexing hg18.fa , I put all...

Hello,

Before indexing hg18.fa , I put all chr1 to chrY including chrM to hg18.fa using this code mention below. When I tried for single chr1 fasta for indexing it runs properly. Is this error due...
Forum: Bioinformatics 09-28-2011, 09:24 PM
Replies: 29
Views: 17,407
Posted By haojam
Hello, I would like to index for aligning...

Hello,

I would like to index for aligning FASTQ sequences to FASTA hg18 reference sequence. The FASTQ sample sequences are SOLID reads. Could you please assist me. I hereby attach the error...
Forum: Bioinformatics 09-28-2011, 09:20 PM
Replies: 29
Views: 17,407
Posted By haojam
Hello, I would like to index for aligning...

Hello,

I would like to index for aligning FASTQ sequences to FASTA

[haojamrocky@melon bwa-0.5.9]$ ./bwa index -a bwtsw -c /home/haojamrocky/DATA/hg18chr/hg18.fasta
[bwa_index] Pack nucleotide...
Forum: Bioinformatics 09-24-2011, 09:30 PM
Replies: 29
Views: 17,407
Posted By haojam
Hi, When I run BWA for aligning fasta chr.1...

Hi,

When I run BWA for aligning fasta chr.1 sequence with fastq SRR reads there is an error as below . Could you plz help me out.

Regards,

[bwa-0.5.9]$ ./bwa aln /home/DATA/chr1.fa...
Forum: Bioinformatics 09-24-2011, 02:15 AM
Replies: 29
Views: 17,407
Posted By haojam
SeqAnswers Group Mr/Mrs., I have installed...

SeqAnswers Group

Mr/Mrs.,
I have installed and make BWA aligner software, but after getting into bwa-0.5.9 folder I get this

COPYING bamlite.c bwa bwase.o bwt_gen ...
Forum: Bioinformatics 06-13-2011, 02:08 AM
Replies: 5
Views: 2,385
Posted By haojam
Hello Dear, After installing MAQ by typing Sudo...

Hello Dear,
After installing MAQ by typing Sudo apt-get install.maq at UBUNTO in linux platform do I need to compile and make for running the program.
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