SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 22 of 22
Search took 0.00 seconds.
Search: Posts Made By: chiayi
Forum: Bioinformatics 05-12-2017, 08:38 AM
Replies: 90
Views: 14,559
Posted By chiayi
Hi Brian, Thank you so much for all the...

Hi Brian,

Thank you so much for all the troubleshooting and effort. I really appreciate it.

I also worked with our IT and found that the slow down when I set -Xmx to ~80% of physical memeory...
Forum: Bioinformatics 05-06-2017, 06:19 AM
Replies: 90
Views: 14,559
Posted By chiayi
I tried to tune several places and here's a...

I tried to tune several places and here's a summary of what I found:
1.
Executing clump.Clumpify [-Xmx16g, in=in.fastq.gz, out=out.fq.gz, dedupe, reorder]

[dedupe reorder][to reproduce Brian's...
Forum: Bioinformatics 05-04-2017, 08:50 PM
Replies: 90
Views: 14,559
Posted By chiayi
1) 37.17 2) 4) I changed the RAM to get the job...

1) 37.17
2) 4) I changed the RAM to get the job start sooner. You are certainly right, the setting should be identical. I started another run using the same mem and this time it still stuck at the...
Forum: Bioinformatics 05-04-2017, 06:02 PM
Replies: 90
Views: 14,559
Posted By chiayi
It was at the 'Deduping' step. I removed reorder...

It was at the 'Deduping' step. I removed reorder tag and it still stuck at the same step:

openjdk version "1.8.0_121"
OpenJDK Runtime Environment (build 1.8.0_121-b13)
OpenJDK 64-Bit Server VM...
Forum: Bioinformatics 05-04-2017, 12:00 PM
Replies: 90
Views: 14,559
Posted By chiayi
1) pigz is in my path. *Updated* When I...

1) pigz is in my path.
*Updated* When I monitored a running job, here's what I saw:
PR NI VIRT RES SHR S %CPU %MEM TIME+ COMMAND
20 0 56.006g 0.028t 13060 S 100.3 22.8 343:27.03...
Forum: Bioinformatics 05-04-2017, 09:48 AM
Replies: 90
Views: 14,559
Posted By chiayi
Hi Brian, Thank you for adding these new...

Hi Brian,

Thank you for adding these new features. I tried clumpify (37.17) to detect duplicates in the HiSeq 2500 single-ended strand-specific 50 bp reads. My pipeline is...
Forum: Bioinformatics 12-17-2016, 07:41 AM
Replies: 646
Views: 130,072
Posted By chiayi
For maaping diploid maize data, I concatenated...

For maaping diploid maize data, I concatenated all the chromosomes for a given species (e.g. 10 chr in maize) and used it as the mapping reference. I then mapped the BBDuk-trimmed reads to this...
Forum: Bioinformatics 12-17-2016, 06:25 AM
Replies: 90
Views: 14,559
Posted By chiayi
I would love that. I will send the access to you...

I would love that. I will send the access to you in message momentarily. Thank you so much!
Forum: Bioinformatics 12-16-2016, 07:22 PM
Replies: 646
Views: 130,072
Posted By chiayi
I share your thoughts so I will at least try a...

I share your thoughts so I will at least try a few background to see how it goes. On the other hand, I'm not sure how to compare the accuracy between the results generated from base reference vs SNP...
Forum: Bioinformatics 12-16-2016, 07:12 PM
Replies: 90
Views: 14,559
Posted By chiayi
Thank you so much for the thorough explanation. I...

Thank you so much for the thorough explanation. I tried a couple things and please find the reports as follows:



I'm not sure about the answers to these two questions. I will need to ask around...
Forum: Bioinformatics 12-16-2016, 04:43 PM
Replies: 90
Views: 14,559
Posted By chiayi
Hello Brian, I started to use clumpify and...

Hello Brian,

I started to use clumpify and the size was on average reduced ~25% for NextSeq Arabidopsis data. Thanks for the development!

In a recent run for HiSeq maize data, I got an error...
Forum: RNA Sequencing 12-15-2016, 02:37 PM
Replies: 18
Views: 2,669
Posted By chiayi
@Brian, @GenoMax, Thanks for all the...

@Brian, @GenoMax,
Thanks for all the clarification. It's very helpful.
It turned out my original issue was solely caused by the descripancy in the genome name. The latest version of featureCounts...
Forum: RNA Sequencing 12-15-2016, 06:00 AM
Replies: 18
Views: 2,669
Posted By chiayi
I was referring to the trd (trimreaddescription)...

I was referring to the trd (trimreaddescription) option in reformat. I thought that would clean the fasta header after the first space, or did I misunderstand?
Forum: RNA Sequencing 12-15-2016, 05:39 AM
Replies: 18
Views: 2,669
Posted By chiayi
@Michael: I used sed to clean up the chromosome...

@Michael: I used sed to clean up the chromosome name in each alignment in the SAM. featureCounts works fine after that. Thank you so much.
@GenoMax: Thanks for the suggestion.
BTW, does reformat.sh...
Forum: RNA Sequencing 12-15-2016, 03:45 AM
Replies: 18
Views: 2,669
Posted By chiayi
@GenoMax BBMap version 36.62 featureCounts...

@GenoMax
BBMap version 36.62
featureCounts v1.5.1
Thank you.
Forum: Bioinformatics 12-14-2016, 09:11 PM
Replies: 646
Views: 130,072
Posted By chiayi
Hi Brian and other members, I'm trying to...

Hi Brian and other members,

I'm trying to map the Illumina reads generated from 19 inbred and hybrid mazie cultivars under two conditions for downstream differential expression analysis....
Forum: RNA Sequencing 12-14-2016, 08:20 PM
Replies: 18
Views: 2,669
Posted By chiayi
On a related note, I encountered this issue even...

On a related note, I encountered this issue even after reformat.

The sam file was generated by BBMap,

bbmap.sh -Xmx32g in1=r1.BBDuk.fastq.gz in2=r2.BBDuk.fastq.gz maxindel=2000 outm=mapped.sam...
Forum: Bioinformatics 12-04-2016, 10:53 AM
Replies: 304
Views: 80,155
Posted By chiayi
Hi Brian, bzip2 was in my path yet pbzip2...

Hi Brian,

bzip2 was in my path yet pbzip2 was not. As you predicted, when I checked the status using "top -c" a java was hanging around with 0 cpu utilization. I intalled pbzip2 and the issue was...
Forum: Bioinformatics 12-03-2016, 05:37 PM
Replies: 304
Views: 80,155
Posted By chiayi
Sure. This is where the run would...

Sure.



This is where the run would stuck.
Forum: Bioinformatics 12-03-2016, 03:01 PM
Replies: 304
Views: 80,155
Posted By chiayi
Hi Brian, Thank you again. That was very...

Hi Brian,

Thank you again. That was very helpful. One last quesiton, is bz2 not compatible with BBDuk? Some of my files are bz2 and for those runs it looked like the files were not loaded and the...
Forum: Bioinformatics 12-03-2016, 02:06 PM
Replies: 304
Views: 80,155
Posted By chiayi
Thank you, Brian. I guess I was confused with...

Thank you, Brian. I guess I was confused with adapter trimming and adapter filtering, and it's clear now with your explanation. I have a follow-up question. I thought the percentage of reads with...
Forum: Bioinformatics 12-02-2016, 08:57 PM
Replies: 304
Views: 80,155
Posted By chiayi
Hi Brian, I just started to try BBDuk after...

Hi Brian,

I just started to try BBDuk after being too used to the alternative trimmer and would like some stimulant. I found the functions in BBTools comprehensive and sophisticated. Thank you!
...
Showing results 1 to 22 of 22

 


All times are GMT -8. The time now is 02:06 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2018, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO