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Forum: Bioinformatics 02-25-2016, 05:25 PM
Replies: 12
Views: 2,964
Posted By harrike
Hi biokloot, To me, all "-1" does suppress...

Hi biokloot,

To me, all "-1" does suppress all SJ, as "-1 means no output for that motif". But I am not sure how a read spanning an intron will be mapped in this case.

I am sure Alex will give...
Forum: Bioinformatics 02-19-2016, 07:52 PM
Replies: 218
Views: 143,532
Posted By harrike
Hi Alex, Thanks for your suggestions. I...

Hi Alex,

Thanks for your suggestions.

I manually checked a couple of reads as Genomax suggested, and find the major reason of this low mapping rate is because that most of the reads have...
Forum: Bioinformatics 02-19-2016, 06:31 AM
Replies: 218
Views: 143,532
Posted By harrike
Hi Alex, This time I am using STAR to...

Hi Alex,

This time I am using STAR to another set of data, which are strand-specific, paired-end, and of 150 bp read length. The command I used is "

STAR-STAR_2.4.2a/bin/Linux_x86_64/STAR...
Forum: Bioinformatics 02-16-2016, 01:54 PM
Replies: 218
Views: 143,532
Posted By harrike
Hi Genomax, Thanks for providing the info....

Hi Genomax,

Thanks for providing the info. It is quite helpful. I am clear now.

Rui
Forum: Bioinformatics 02-16-2016, 01:44 PM
Replies: 218
Views: 143,532
Posted By harrike
Does the 2nd column indicate the strand? I check...

Does the 2nd column indicate the strand? I check a few lines of my data. The frequency and number (2nd column value) are listed below.

Frequency Number
847 147
75 163
902 339
...
Forum: Bioinformatics 02-16-2016, 01:16 PM
Replies: 218
Views: 143,532
Posted By harrike
Hi Alex, I have a simple question that is...

Hi Alex,

I have a simple question that is tell the strand of a read mapped to (strand-specific data). I viewed my output .bam file using "sambamba view". Is it possible to tell tell the strand...
Forum: Bioinformatics 02-12-2016, 09:12 PM
Replies: 2
Views: 1,020
Posted By harrike
Hi GenoMax, Thanks for your reply. Somehow I...

Hi GenoMax,

Thanks for your reply. Somehow I am not able to install the RSeQC.

I referred to this thread ---...
Forum: Bioinformatics 02-12-2016, 02:53 PM
Replies: 2
Views: 1,020
Posted By harrike
Question about RNA-seq read strand

Hi All,

I downloaded a few public RNA-seq data, and mapped them to the genome and viewed in IGV . As I don't know if the libraries were constructed strand-specifically. Is it possible to judge...
Forum: Bioinformatics 02-11-2016, 10:23 AM
Replies: 12
Views: 2,964
Posted By harrike
Hi Alex, Great, thanks for your...

Hi Alex,

Great, thanks for your clarification.

I decide to using the filter "--outSJfilterCountUniqueMin -1 -1 -1 -1 --outSJfilterCountTotalMin 10 10 10 10" for my 2nd-pass mapping.

Rui
Forum: Bioinformatics 02-10-2016, 07:48 PM
Replies: 2
Views: 856
Posted By harrike
Hi nimrod337, If I was you, I would just use...

Hi nimrod337,

If I was you, I would just use the "super.gtf". First, the cuffmerged (from 24 samples) super.gtf gives you the most complete transcript annotation, which should include all the...
Forum: Bioinformatics 02-10-2016, 07:14 PM
Replies: 12
Views: 2,964
Posted By harrike
Hi Alex, Thanks for your explanation. I...

Hi Alex,

Thanks for your explanation. I tried the combination of "--outSJfilterCountUniqueMin -1 -1 -1 -1 --outSJfilterCountTotalMin 10 10 10 10", it works. It has only half of the junctions...
Forum: Bioinformatics 02-09-2016, 06:58 PM
Replies: 12
Views: 2,964
Posted By harrike
Hi Alex, I tried one of my libraries, using...

Hi Alex,

I tried one of my libraries, using the "--outSJfilterCountTotalMin 10 10 10 10 --outFilterType BySJout". In the *SJ.out.tab file, some of the junctions are still of <10 reads support (see...
Forum: Bioinformatics 02-09-2016, 06:13 PM
Replies: 12
Views: 2,964
Posted By harrike
Hi Alex, Great ! Thank you very much for...

Hi Alex,

Great ! Thank you very much for your reply. I am testing those settings.

I am curious about what happens to those uniquely mapped reads spanning a junction with <10 reads support. Are...
Forum: Bioinformatics 02-08-2016, 01:06 PM
Replies: 12
Views: 2,964
Posted By harrike
STAR coupled with Cufflinks

I am working on a plant, in which the genome has been sequenced but the gene-annotation quality are not as good as I expected. I am trying to use STAR and Cufflinks to annotate novel transcripts from...
Forum: Bioinformatics 05-09-2011, 07:24 AM
Replies: 514
Views: 213,298
Posted By harrike
I am using the apple genome which is about 750...

I am using the apple genome which is about 750 mb.

Actually, I tried the mapping several times. At the beginning, the size of the output file kept increasing and the Bowtie command only took about...
Forum: Bioinformatics 05-09-2011, 07:02 AM
Replies: 514
Views: 213,298
Posted By harrike
Thanks, Sdvie. It my Mac which has 16 cores...

Thanks, Sdvie.

It my Mac which has 16 cores and 32 GB. I don't use remote control.
Forum: Bioinformatics 05-09-2011, 06:34 AM
Replies: 514
Views: 213,298
Posted By harrike
Here maybe the best place for my question. ...

Here maybe the best place for my question.

I am trying to use Bowtie to map about 300,000 reads to my reference. I use the command: bowtie -a -v 0 -p 10 -t INDEX_FILE -f READS_FILE.fasta >...
Forum: Bioinformatics 05-09-2011, 06:29 AM
Replies: 1
Views: 1,368
Posted By harrike
My computer has 16 cores and 32 GB memory, and is...

My computer has 16 cores and 32 GB memory, and is using Mac OS X system.
Forum: Bioinformatics 05-09-2011, 06:18 AM
Replies: 1
Views: 1,368
Posted By harrike
Bowtie mapping problem

I am trying to use Bowtie to map about 300,000 reads to my reference. I use the command: bowtie -a -v 0 -p 10 -t INDEX_FILE -f READS_FILE.fasta > RESULT_FILE --un unmapped.txt.

The command...
Forum: General 04-14-2011, 09:18 AM
Replies: 1
Views: 2,576
Posted By harrike
How to assign more CPU cores to terminal on Mac?

Hi, all,

When running perl scripts on our Mac (our super computer with 16 CPU cores and 32 GB RAM), I found only one core is in process (100%). Other 15 cores are less than 5%. I feel the speed...
Forum: Bioinformatics 04-13-2011, 04:34 AM
Replies: 3
Views: 2,762
Posted By harrike
commercial software: CLC genome workbench....

commercial software: CLC genome workbench. www.clcbio.com. It is quite expensive.

There are many free software shared in this community. You'd better use "search" to get what you want.
Forum: Bioinformatics 04-01-2011, 06:29 PM
Replies: 0
Views: 1,280
Posted By harrike
Weird file compression

Today I had a .fasta file compressed to .zip file. The original 200 Mb file come to only 2 Mb. It's 100 times smaller. Is this possible? or something wrong?
Forum: Bioinformatics 01-09-2011, 07:13 AM
Replies: 9
Views: 6,431
Posted By harrike
IIia, Thank you for your reply. You answer...

IIia,

Thank you for your reply. You answer is quite helpful to me.

Actually, my lab has bought the CLC workbench, which is not available to me now since I am out of the lab for a period. I just...
Forum: Bioinformatics 01-08-2011, 05:56 PM
Replies: 9
Views: 6,431
Posted By harrike
Novel question---What's .qual file for?

Recently I got my sequencing data based on SOLiD system. For each sample I got two .csfasta files labled 1 and 2, and two .qual files corresponding to the csfasta file. Since I am quite new to this...
Forum: SOLiD 01-03-2011, 06:15 AM
Replies: 36
Sticky: SOLiD Adapters
Views: 42,561
Posted By harrike
Thank you very much. That's exactly what i want.:p

Thank you very much. That's exactly what i want.:p
Showing results 1 to 25 of 29

 


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