SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 25 of 235
Search took 0.03 seconds.
Search: Posts Made By: shi
Forum: Bioinformatics 03-22-2017, 04:01 PM
Replies: 12
Views: 2,372
Posted By shi
Thanks for sending us an example bam file,...

Thanks for sending us an example bam file, @GenoMax. We found there were some tags added into the chr field in the bam file, which led to the crash of featureCounts. Below are the first two reads in...
Forum: Bioinformatics 03-19-2017, 06:00 PM
Replies: 12
Views: 2,372
Posted By shi
Sorry about this. Could you please try out the...

Sorry about this. Could you please try out the latest version we released a couple of days ago? If the problem persists, we will need to take a look at the data.
Forum: Bioinformatics 10-31-2016, 02:37 PM
Replies: 154
Views: 57,956
Posted By shi
Are you using the latest version? '-b' is an...

Are you using the latest version? '-b' is an invalid argument. Could you also provide the assignment summary that can be found in the 'countsSb10.txt.summary' file?
Forum: RNA Sequencing 09-11-2016, 05:03 PM
Replies: 4
Views: 1,652
Posted By shi
In terms of aligner choice for mapping RNA-seq...

In terms of aligner choice for mapping RNA-seq data, you may take a look at this paper that just came out this week:

http://www.ncbi.nlm.nih.gov/pubmed/27592709
Forum: Bioinformatics 09-08-2016, 05:14 PM
Replies: 8
Views: 1,590
Posted By shi
Does hsa-miR-92a overlap with other miRNAs? If a...

Does hsa-miR-92a overlap with other miRNAs? If a read overlaps with more than one miRNA, featureCounts wouldnt count it.
Forum: Bioinformatics 09-08-2016, 04:06 PM
Replies: 8
Views: 1,590
Posted By shi
Most of your reads did not hit any miRNA listed...

Most of your reads did not hit any miRNA listed in your provided annotation and therefore they were not counted by featureCounts (Unassigned_NoFeatures 17288648).

If your annotation only includes...
Forum: Bioinformatics 09-08-2016, 03:23 PM
Replies: 8
Views: 1,590
Posted By shi
Can you show the counting summary generated by...

Can you show the counting summary generated by featureCounts - you can find it in the '.summary' file generated by featureCounts?
Forum: Bioinformatics 08-28-2016, 10:23 PM
Replies: 24
Views: 7,235
Posted By shi
Can you update to Subread 1.5.1 and try again?

Can you update to Subread 1.5.1 and try again?
Forum: RNA Sequencing 08-25-2016, 03:30 PM
Replies: 6
Views: 1,554
Posted By shi
featureCounts uses 'NH' tag to identify...

featureCounts uses 'NH' tag to identify multi-mapping reads. So you have a lot of reads with this tag having a value greater than 1 in your mapping result.
Forum: RNA Sequencing 08-23-2016, 03:18 PM
Replies: 6
Views: 1,554
Posted By shi
What featureCounts does is it counts the number...

What featureCounts does is it counts the number of reads overlapping with features included in the annotation. Reads that were reported as mapped by aligner but not overlapping any features will not...
Forum: Bioinformatics 06-08-2016, 04:49 PM
Replies: 6
Views: 1,691
Posted By shi
featureCounts is also available in Bioconductor R...

featureCounts is also available in Bioconductor R package Rsubread:

http://bioconductor.org/packages/release/bioc/html/Rsubread.html
Forum: Bioinformatics 06-05-2016, 09:29 PM
Replies: 154
Views: 57,956
Posted By shi
Read 1 was reported only once in your mapping...

Read 1 was reported only once in your mapping result and this read was found to overlap with two genes (ENSNNNG00000079745 and ENSNNNG00000059028) by featureCounts.

Read 2 was reported 5 times in...
Forum: Bioinformatics 04-13-2016, 03:36 PM
Replies: 8
Views: 1,160
Posted By shi
It is written in C (not C++ or java).

It is written in C (not C++ or java).
Forum: Bioinformatics 03-31-2016, 03:02 PM
Replies: 7
Views: 1,657
Posted By shi
Thanks for providing the info. Can you also send...

Thanks for providing the info. Can you also send us the fastq files so that we can reproduce the problem and find out what went wrong?
Best,
Wei
Forum: Bioinformatics 03-23-2016, 02:49 PM
Replies: 7
Views: 1,657
Posted By shi
Could you please provide the screen output and...

Could you please provide the screen output and also your commands? Subread has no problems to process more than 35 million reads.
Forum: Bioinformatics 03-22-2016, 05:20 PM
Replies: 4
Views: 1,039
Posted By shi
I noticed that the '—t' option in your command...

I noticed that the '—t' option in your command includes a long dash, which is invalid. Could you replace it with a hyphen and then reran your command? This invalid option might cause problems for...
Forum: Bioinformatics 03-21-2016, 03:04 PM
Replies: 4
Views: 1,039
Posted By shi
Hi, are you using the latest version (1.5.0-p1)?

Hi, are you using the latest version (1.5.0-p1)?
Forum: Bioinformatics 03-21-2016, 02:58 PM
Replies: 1
Views: 1,272
Posted By shi
The align() function in Bioconductor package...

The align() function in Bioconductor package Rsubread allows you to provide multiple input files for alignment at the same time:

http://bioconductor.org/packages/release/bioc/html/Rsubread.html
...
Forum: RNA Sequencing 03-09-2016, 01:20 PM
Replies: 8
Views: 2,917
Posted By shi
featureCounts works with both GTF and GFF...

featureCounts works with both GTF and GFF formats. I think it should be fine if you directly provide your GFF3 annotation to featureCounts program.
Forum: Bioinformatics 03-06-2016, 01:40 PM
Replies: 2
Views: 1,104
Posted By shi
Could you show the content of the ".summary" file...

Could you show the content of the ".summary" file which was part of featureCounts output?
Forum: Bioinformatics 02-24-2016, 12:52 PM
Replies: 24
Views: 7,235
Posted By shi
What is the version of featureCounts you use?

What is the version of featureCounts you use?
Forum: Epigenetics 01-26-2016, 03:48 PM
Replies: 3
Views: 1,814
Posted By shi
With featureCounts, the default setting is...

With featureCounts, the default setting is unstranded read counting (-s 0).

If you performed unstranded sequencing, the percentage of sense strand reads should be similar to that of antisense...
Forum: Bioinformatics 01-03-2016, 04:11 PM
Replies: 24
Views: 7,235
Posted By shi
That's great. Thanks for letting us know.

That's great. Thanks for letting us know.
Forum: Bioinformatics 12-01-2015, 12:41 PM
Replies: 5
Views: 1,902
Posted By shi
Sure. Maybe via dropbox? Or you can put it...

Sure. Maybe via dropbox? Or you can put it somewhere on internet and then we can download it.
Forum: Bioinformatics 11-29-2015, 07:01 PM
Replies: 5
Views: 1,902
Posted By shi
Could you send it via CloudStor? ...

Could you send it via CloudStor?

https://cloudstor.aarnet.edu.au/
Showing results 1 to 25 of 235

 


All times are GMT -8. The time now is 06:27 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO