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Forum: Bioinformatics 12-08-2018, 03:52 PM
Replies: 0
Views: 449
Posted By sbdk82
command line BLASTP with description

How can I get the description( first column in the figure) when I run the command line blastp?
I am using the following options
-outfmt "6 std qlen slen"

http://i68.tinypic.com/9a34oo.jpg
Forum: Bioinformatics 09-22-2014, 12:29 PM
Replies: 7
Views: 2,604
Posted By sbdk82
Thanks !!! I will try that

Thanks !!! I will try that
Forum: Bioinformatics 09-22-2014, 12:23 PM
Replies: 7
Views: 2,604
Posted By sbdk82
So I should try with this? #SBATCH --nodes=1...

So I should try with this?

#SBATCH --nodes=1
#SBATCH --ntasks-per-node=1
#SBATCH --time=120:00:00
#SBATCH --mem=100g
Forum: Bioinformatics 09-22-2014, 12:10 PM
Replies: 7
Views: 2,604
Posted By sbdk82
I think it uses total 500 gb (100gb x 5 nodes)...

I think it uses total 500 gb (100gb x 5 nodes) for this job. It does not distribute different files into different nodes.
Forum: Bioinformatics 09-22-2014, 10:50 AM
Replies: 7
Views: 2,604
Posted By sbdk82
STAR Aligner

I am running STAR for aligning wheat RNA-Seq data with Ensemble reference file . The size of reference file is 4gb. The genome directory created in the first step is 42 gb. The mapping step took more...
Forum: Bioinformatics 09-16-2014, 10:08 AM
Replies: 8
Views: 2,195
Posted By sbdk82
I see. Thanks !!

I see. Thanks !!
Forum: Bioinformatics 09-16-2014, 10:00 AM
Replies: 8
Views: 2,195
Posted By sbdk82
I am using the latest version(2.3.0.1) . Yes, I...

I am using the latest version(2.3.0.1) . Yes, I saw some other people are also getting seg fault. I will post that on google group. Anyway, Thanks a lot for your help :)
Forum: Bioinformatics 09-16-2014, 09:45 AM
Replies: 8
Views: 2,195
Posted By sbdk82
Thanks !! I will try that. I used the...

Thanks !! I will try that.

I used the original SAM as you suggested in an earlier post, but that gave me some error. So I tried with sorted sam. I am using BWA-MEM because tophat2 cannot handle...
Forum: Bioinformatics 09-16-2014, 09:30 AM
Replies: 8
Views: 2,195
Posted By sbdk82
I used BWA-MEM for alignment. Then used samtools...

I used BWA-MEM for alignment. Then used samtools to sort the SAM file using this

samtools view -b -S File.SAM > File.BAM
samtools sort -n File.BAM File_sorted
samtools view -h ...
Forum: Bioinformatics 09-16-2014, 08:09 AM
Replies: 8
Views: 2,195
Posted By sbdk82
HTSeq warning message

I am using HTSeq-count to count paired end reads (2 samples with 3 replicates in each) . But I am getting the warning message which says "some reads with missing mates encountered". Am I doing...
Forum: Bioinformatics 09-09-2014, 08:22 AM
Replies: 2
Views: 1,879
Posted By sbdk82
Thanks Devon !! So I should use the...

Thanks Devon !!

So I should use the following to build the index

STAR --runMode genomeGenerate --genomeDir <output directory> --genomeFastaFiles /path/reference.fa --runThreadN 5 --sjdbGTFfile...
Forum: Bioinformatics 09-08-2014, 07:10 PM
Replies: 2
Views: 1,879
Posted By sbdk82
STAR for alignment

I am trying to use STAR instead of Tophat, but I am bit confused. I already have the reference file and GTF file. So should I skip the "generate genome" and "generate genome with annotation" steps (4...
Forum: Bioinformatics 08-27-2014, 06:54 AM
Replies: 7
Views: 1,672
Posted By sbdk82
Thanks Ryan !! I got it now, I need to do the...

Thanks Ryan !! I got it now, I need to do the following

If I am using
samtools sort file.bam file_sorted
then I should use "-r pos"
and if I am using
samtools sort -n file.bam file_sorted...
Forum: Bioinformatics 08-26-2014, 01:00 PM
Replies: 7
Views: 1,672
Posted By sbdk82
Thanks for the reply. I used following for...

Thanks for the reply.

I used following for converting sam to bam and sorting the bam

samtools view -b -S file.sam > file.bam
samtools sort file.bam file_sorted
samtools view -h ...
Forum: Bioinformatics 08-26-2014, 10:13 AM
Replies: 7
Views: 1,672
Posted By sbdk82
HTSeq Counting Warning

Hello

I am getting lots of warning messages when I run HTSeq-count. I saw few other posts on this forum, but could not figure out the solution.

I am using paired-end illumina sequences. I have...
Forum: Bioinformatics 08-18-2014, 11:39 AM
Replies: 9
Views: 3,245
Posted By sbdk82
Thanks again !!

Thanks again !!
Forum: Bioinformatics 08-18-2014, 10:19 AM
Replies: 9
Views: 3,245
Posted By sbdk82
Thanks Brian and GenoMax

Thanks Brian and GenoMax
Forum: Bioinformatics 08-18-2014, 09:50 AM
Replies: 9
Views: 3,245
Posted By sbdk82
illumina paired-end data

I have paired-end illumina data for some RNA-Seq analysis. There are four fasta files and are named like this.

XXX_XXXXXX_L001_R1_001.fastq XXX_XXXXXX_L001_R2_001.fastq ...
Forum: RNA Sequencing 08-16-2014, 06:04 AM
Replies: 2
Views: 2,045
Posted By sbdk82
Thanks Yu !! Actually I have two samples of...

Thanks Yu !!

Actually I have two samples of data with three replicates in each sample. Thus I have 6 fasta files. So each data file represented by qi (i = 1,2 ..6) ? I used cufflink and then...
Forum: RNA Sequencing 08-15-2014, 09:17 AM
Replies: 2
Views: 2,045
Posted By sbdk82
Cuffdiff output

I am running BWA->cufflink for differential gene expression and the cuffdiff output contains many repeated gene_ids. For example:


test_id gene_id gene locus sample_1 sample_2 status...
Forum: Bioinformatics 07-16-2014, 07:40 AM
Replies: 3
Views: 784
Posted By sbdk82
It was working fine when I used Bowtie2 with long...

It was working fine when I used Bowtie2 with long index option, but the index files have suffixes .bt21 which are not recognized by tophat. I asked that question in another thread, but someone...
Forum: Bioinformatics 07-16-2014, 07:37 AM
Replies: 3
Views: 784
Posted By sbdk82
I am working on Triticum aestivum. I got the...

I am working on Triticum aestivum. I got the reference from Ensemble site ftp://ftp.ensemblgenomes.org/pub/plants/release-22/fasta/triticum_aestivum/dna/
Forum: Bioinformatics 07-15-2014, 07:49 PM
Replies: 3
Views: 784
Posted By sbdk82
Tophat Error

I am getting the following error when I use bowtie and bowtie2

Error: Reference sequence has more than 2^32-1 characters! Please divide the
reference into batches or chunks of about 3.6 billion...
Forum: Bioinformatics 07-15-2014, 06:21 PM
Replies: 5
Views: 3,427
Posted By sbdk82
Yes, I am using tophat/2.0.12 but still getting...

Yes, I am using tophat/2.0.12 but still getting that error. Anyway, thanks for your reply.
Forum: Bioinformatics 07-15-2014, 03:59 PM
Replies: 5
Views: 3,427
Posted By sbdk82
Bowtie2 long index(.bt21) and tophat

I am using tophat2 with long index with suffixes .bt21. But it is giving the following error

Could not find Bowtie 2 index files (.*.bt2)
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