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Search: Posts Made By: genomeHunter
Forum: Bioinformatics 07-25-2013, 08:44 AM
Replies: 14
Views: 5,862
Posted By genomeHunter
If you have multiple cores, this could be even...

If you have multiple cores, this could be even better:

find . -name *.sra | xargs -P $NUM_CORES -n 1 fastq-dump

My disk can easily handle 16 simultaneous dumps.

Cheers,
GH
Forum: Bioinformatics 07-20-2013, 08:10 AM
Replies: 11
Views: 3,062
Posted By genomeHunter
Do you have any rough speedup factors? I tried ...

Do you have any rough speedup factors? I tried

samtools view -buS exp.sam | samtools sort -@ 16 -m 4G - sorted

And it takes 10 minutes for a moderate size SAM file.

Cheers,
GH
Forum: Bioinformatics 07-19-2013, 04:42 PM
Replies: 11
Views: 3,062
Posted By genomeHunter
I am not 100% sure but it must be 6 Gbps SAS. ...

I am not 100% sure but it must be 6 Gbps SAS.

GH
Forum: Bioinformatics 07-19-2013, 03:48 PM
Replies: 11
Views: 3,062
Posted By genomeHunter
Thanks. I am using 4GB/threads and 16 threads....

Thanks. I am using 4GB/threads and 16 threads. Our main disk is a 12-disk RAID-6 arrays with enterprise-level HDDs.

Do you know how does samtools sort compare to SortSam and NovoSort?

Cheers,...
Forum: Bioinformatics 07-19-2013, 01:45 PM
Replies: 11
Views: 3,062
Posted By genomeHunter
I tried it on a moderate-sized BAM file and it...

I tried it on a moderate-sized BAM file and it was not very fast on our mini-server (32 Cores and RAID-6 disk). I guess I will be using xargs :-)

Cheers,
GH
Forum: Bioinformatics 07-19-2013, 12:58 PM
Replies: 11
Views: 3,062
Posted By genomeHunter
No, I was not. I saw the "-@" option in a fork of...

No, I was not. I saw the "-@" option in a fork of samtools, I guess it was called samtools-mt. I did not know it was added to samtools.

Thanks,
GH
Forum: Bioinformatics 07-19-2013, 12:31 PM
Replies: 11
Views: 3,062
Posted By genomeHunter
Fast BAM sorting

Hello,

I have lots of unsorted BAM files and the sorting process is very slow. One solution I could think of was to run multiple instances of samtools:

cat files.txt | xargs -n 1 -P...
Forum: Bioinformatics 07-03-2013, 07:17 PM
Replies: 44
Views: 32,416
Posted By genomeHunter
Hi Heng, Thanks for your post. It would be...

Hi Heng,

Thanks for your post. It would be nice if you could upload the false spliced-reads somewhere. You can see my own comparison with BWA and Bowtie2 in GCAT (link...
Forum: Bioinformatics 07-01-2013, 10:23 AM
Replies: 44
Views: 32,416
Posted By genomeHunter
Thanks. I knew about that and actually I use it...

Thanks. I knew about that and actually I use it to filter unique reads, but it is just a flag and not an indicator of mapping quality. In contrast, as you mentioned, BWA assignes a MAPQ based on...
Forum: Bioinformatics 06-29-2013, 10:15 PM
Replies: 44
Views: 32,416
Posted By genomeHunter
STAR's MAPQ values should NOT be used for...

STAR's MAPQ values should NOT be used for filtering reads and judging their qualities. I saw Heng's ROC plot in which STAR's ROC was just a single dot. I tried Bioplanet's GCAT test set on STAR and...
Forum: Bioinformatics 05-30-2013, 06:58 PM
Replies: 23
Views: 31,760
Posted By genomeHunter
Solution

I think I have finally found the solution!

Some new SRA files need refseq for dumping. It should be in ~/ncbi/public/refseq (default path). For some reason, my SRA toolkit was unable to download...
Forum: Bioinformatics 05-29-2013, 06:21 PM
Replies: 23
Views: 31,760
Posted By genomeHunter
I have tried everything, in every forum, and in...

I have tried everything, in every forum, and in every thread.

I simply cannot understand why such a presumably simple and tiny application could cause so much headache. It just cannot be solved...
Forum: Bioinformatics 05-29-2013, 05:38 PM
Replies: 23
Views: 31,760
Posted By genomeHunter
Hello, I am also trying to dump the new...

Hello,

I am also trying to dump the new reference-based SRA files. It has been driving me nuts, as it is impossible to get to work. Some NBCI staff are very friendly and are trying to help but it...
Forum: Bioinformatics 05-25-2013, 09:28 AM
Replies: 3
Views: 3,171
Posted By genomeHunter
SRA decryption help

Dear all,

I have a couple of *.sra.ncbi_enc files and I am trying to decrypt them; however, NCBI website is very confusing:

1. Here...
Forum: Bioinformatics 05-15-2013, 08:12 PM
Replies: 12
Views: 13,639
Posted By genomeHunter
Thank you so much! Your answer was enlightening....

Thank you so much! Your answer was enlightening. I will probably decrypt them since they are located on a secure server.

Cheers,
GH
Forum: Bioinformatics 05-13-2013, 04:59 AM
Replies: 12
Views: 13,639
Posted By genomeHunter
NCBI archive files are .sra files that are used...

NCBI archive files are .sra files that are used to generate .fastq files. Did you use .sra files?

GH
Forum: Bioinformatics 05-12-2013, 05:01 PM
Replies: 12
Views: 13,639
Posted By genomeHunter
Sra

Hello,

Since you were successful in decrypting, could you please shed light on this comment from (SRA Toolkit (http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=toolkit_doc&f=vdb-decrypt)):
...
Forum: Bioinformatics 04-16-2013, 07:10 AM
Replies: 25
Views: 4,264
Posted By genomeHunter
De novo splicing events

Hi Alex,

I read the paper you introduced and it was interesting. However, I have a major problem: I am interested in isoform quantification or gene expression levels. I am focused on de novo...
Forum: Bioinformatics 04-09-2013, 07:28 AM
Replies: 25
Views: 4,264
Posted By genomeHunter
Thanks Alex! Wow...this seems to be...

Thanks Alex!

Wow...this seems to be prohibitively hard. Say fragments lengths are distributed from 180 to 220. Then, one needs to create 41 reads for each (valid) position in any of the...
Forum: Bioinformatics 04-07-2013, 07:49 PM
Replies: 25
Views: 4,264
Posted By genomeHunter
dietmar13, Did you happen to evaluate GEM as...

dietmar13,

Did you happen to evaluate GEM as well? It occurs to me that GEM and STAR are the two emerging mappers and will be very powerful contenders in near future. I have had very good...
Forum: Bioinformatics 04-07-2013, 07:34 PM
Replies: 25
Views: 4,264
Posted By genomeHunter
Thanks Alex! Seems logical. On a side note,...

Thanks Alex! Seems logical.

On a side note, do you know what is the best approach to generate the unique mappability of all genomic positions? Since I discard multi-mappers and consider only...
Forum: Bioinformatics 04-07-2013, 08:53 AM
Replies: 25
Views: 4,264
Posted By genomeHunter
Very interesting. We have been using STAR because...

Very interesting. We have been using STAR because we found it to be much (~25-50X) faster than Bowtie2, while being more accurate, but we have not tried RUM yet.

Your stats indicate a nearly 50%...
Forum: Bioinformatics 04-07-2013, 06:38 AM
Replies: 25
Views: 4,264
Posted By genomeHunter
Thank you so much Wei! I saw the paper a while...

Thank you so much Wei! I saw the paper a while ago and I will definitely give it a try.

GH
Forum: Bioinformatics 04-06-2013, 10:10 PM
Replies: 25
Views: 4,264
Posted By genomeHunter
Thanks dietmar13. We have tried it, but its slow...

Thanks dietmar13. We have tried it, but its slow and some results are very strange. We also tried Cufflinks with the --GTF-guide option, but it takes a lifetime to run and generates a ton of two-exon...
Forum: Bioinformatics 04-06-2013, 09:59 PM
Replies: 25
Views: 4,264
Posted By genomeHunter
Generating splicing graph

Hello everyone,

I have a set of gapped aligned RNAseq reads and I want to generate the splicing graph. I was wondering if you could introduce a tool.

Cheers,
GH
Showing results 1 to 25 of 26

 


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