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Search: Posts Made By: Haneko
Forum: Bioinformatics 07-01-2010, 05:11 PM
Replies: 24
Views: 3,566
Posted By Haneko
Hi ondovb, Yes, Im running it locally but it...

Hi ondovb,

Yes, Im running it locally but it seems to be stuck at the aligning stage:

Round 1 / 4 (2101986 reads):

Sensitivity 4:

EDIT: I have used strace on the process and...
Forum: Bioinformatics 06-30-2010, 05:19 PM
Replies: 24
Views: 3,566
Posted By Haneko
Hi ondovb, Many thanks for the notes! That...

Hi ondovb,

Many thanks for the notes! That was actually my concern.. My team had a discussion over the running time as we were not looking at Arabidopsis samples.

Which brings me to something...
Forum: Bioinformatics 06-29-2010, 10:39 PM
Replies: 24
Views: 3,566
Posted By Haneko
Hi zee, Oh ok! But I'm dealing with SOLiD...

Hi zee,

Oh ok! But I'm dealing with SOLiD reads now, unfortunately.
Forum: Bioinformatics 06-29-2010, 10:15 PM
Replies: 24
Views: 3,566
Posted By Haneko
Hi jinghanna, Thanks a lot for your help!!

Hi jinghanna,

Thanks a lot for your help!!
Forum: Bioinformatics 06-29-2010, 10:09 PM
Replies: 24
Views: 3,566
Posted By Haneko
Hi jinghanna, Thanks! Just to make sure I've...

Hi jinghanna,

Thanks! Just to make sure I've really understood, could i simply have 3 scripts:

script1 : socs -p -r ref_seq.fa -c xxx.csfasta -q xxx.qual -d output1 -N 3 -n 1
script2 : socs -p...
Forum: Bioinformatics 06-29-2010, 06:20 PM
Replies: 24
Views: 3,566
Posted By Haneko
Hi there, I'm sorry, could you please...

Hi there,

I'm sorry, could you please elaborate on how to run the program on a cluster? I installed it on a cluster with about 40 nodes (i intend to only use maybe 5 or 10 as a test).

Just for...
Forum: Bioinformatics 06-01-2010, 05:27 PM
Replies: 35
Views: 19,940
Posted By Haneko
Hi there, I'm currently using BioScope...

Hi there,

I'm currently using BioScope v1.0.1. May I know what the bug on the statistics is?
Forum: Bioinformatics 05-20-2010, 05:26 PM
Replies: 4
Views: 2,548
Posted By Haneko
Hi Shaun, Many thanks!

Hi Shaun,

Many thanks!
Forum: Bioinformatics 05-19-2010, 09:54 PM
Replies: 4
Views: 2,548
Posted By Haneko
Hi sjackman, I saw from another post you are...

Hi sjackman,

I saw from another post you are one of the authors for ABYSS. I'm having some trouble using the mailing list, for some reason my emails keep bouncing back. I'm new to it so I could be...
Forum: Bioinformatics 05-10-2010, 05:09 PM
Replies: 29
Views: 18,155
Posted By Haneko
Hi Thomas, Yes, bioscope supports spliced...

Hi Thomas,

Yes, bioscope supports spliced alignments. Unfortunately, the rna-seq experiment was not strand specific.

If that's the case, will assigning the wrong strand to an unspliced read...
Forum: Bioinformatics 05-09-2010, 05:18 PM
Replies: 29
Views: 18,155
Posted By Haneko
Hi Thomas, I'm using SOLiD BioScope SAM...

Hi Thomas,

I'm using SOLiD BioScope SAM outputs for input into cufflinks, and it doesn't report the XS:A tag regardless of whether it is spliced or unspliced. My initial assumption was that the XS...
Forum: Bioinformatics 04-28-2010, 05:30 PM
Replies: 33
Views: 9,585
Posted By Haneko
Hi clariet, Actually I've never considered...

Hi clariet,

Actually I've never considered this column to be a factor in filtering, so i can't give you a definite answer. But I think it'd be good to filter away those low quality mappings,...
Forum: Bioinformatics 04-27-2010, 11:02 PM
Replies: 33
Views: 9,585
Posted By Haneko
Sorry, I made it a bit confusing. Yes, the...

Sorry, I made it a bit confusing.

Yes, the alignment score I'm referring to is self-calculated. Not column 5 of mapping quality.
Forum: Bioinformatics 04-27-2010, 10:33 PM
Replies: 33
Views: 9,585
Posted By Haneko
Hmm, I guess it depends on how you see it. I...

Hmm, I guess it depends on how you see it. I noted that the column gives a value of 255 for spliced reads, so it's not really helpful when it comes to spliced alignments. And we've always been...
Forum: Bioinformatics 04-27-2010, 09:59 PM
Replies: 33
Views: 9,585
Posted By Haneko
I'm not sure about that. We've never really...

I'm not sure about that. We've never really looked into mapping quality. The score of 10 i was referring to was the alignment score actually.
Forum: Bioinformatics 04-27-2010, 05:18 PM
Replies: 33
Views: 9,585
Posted By Haneko
Hi there, That is actually not the score,...

Hi there,

That is actually not the score, but the mapping quality (I'm assuming you're referring to column 5 for 255 "score"). For calculation of score, you will have to take the alignment in...
Forum: SOLiD 04-27-2010, 01:07 AM
Replies: 12
Views: 5,329
Posted By Haneko
Just curious, how many bases of gaps can BFast...

Just curious, how many bases of gaps can BFast allow for colorspace reads in alignment?
Forum: Bioinformatics 04-26-2010, 10:22 PM
Replies: 10
Views: 3,941
Posted By Haneko
Thanks! I think the '&' somehow couldn't work the...

Thanks! I think the '&' somehow couldn't work the usual way it did. don't know why though.
Forum: Bioinformatics 04-26-2010, 05:13 PM
Replies: 33
Views: 9,585
Posted By Haneko
Hi, I don't think BioScope outputs 2...

Hi,

I don't think BioScope outputs 2 entries, it should only output 1 entry for each alignment (continuous or spliced), unless there are more than one alignment for that read. It shouldn't be...
Forum: Bioinformatics 04-25-2010, 10:06 PM
Replies: 10
Views: 3,941
Posted By Haneko
Hi, I'm also trying out velvet with Illumina...

Hi,

I'm also trying out velvet with Illumina paired-end reads. A few problems I'm facing right now:

1. What should the input be like? I have read 1 and read 2 for the paired-end reads. Do I...
Forum: Bioinformatics 04-14-2010, 05:14 PM
Replies: 29
Views: 18,155
Posted By Haneko
The strand is 'encoded' in hexadecimal within the...

The strand is 'encoded' in hexadecimal within the field values. So to get the strand information, you will have to do an "AND" operation on the flag field.

In the SAM definition for the flag...
Forum: Bioinformatics 04-13-2010, 10:10 PM
Replies: 29
Views: 18,155
Posted By Haneko
Hi there, I believe the second column (the...

Hi there,

I believe the second column (the flag field. For more information, please refer to SAM format definition) contains the strand information. So you could write a script to determine the...
Forum: Bioinformatics 04-07-2010, 07:21 PM
Replies: 10
Views: 10,081
Posted By Haneko
Hi, I'm encountering a similar issue with...

Hi, I'm encountering a similar issue with cuffcompare. While trying to run it with the transcripts.gtf generated from cufflinks, it gave me the following error:

GList error (GList.hh:592):Invalid...
Forum: Bioinformatics 04-07-2010, 07:04 PM
Replies: 1
Views: 1,592
Posted By Haneko
Flux capacitor

Hi, just wondering if anyone has tried using 'Flux Capacitor' for RNA-seq reads? I'm trying it out but need some help.

Thanks!
Forum: Bioinformatics 03-22-2010, 07:10 PM
Replies: 33
Views: 9,585
Posted By Haneko
no, actually. it's because i directly copied it...

no, actually. it's because i directly copied it from the window of my ssh. So there aren't any line breaks there. sorry for the confusion.
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