SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 25 of 40
Search took 0.00 seconds.
Search: Posts Made By: moistplus
Forum: Bioinformatics 01-12-2017, 09:06 AM
Replies: 50
Views: 25,295
Posted By moistplus
Do you have a paper or something like this which...

Do you have a paper or something like this which explain the algorithm behind bbnorm ?
Forum: Bioinformatics 12-16-2016, 03:04 AM
Replies: 98
Views: 26,237
Posted By moistplus
For output, this is out1 and out2 or oute1 and...

For output, this is out1 and out2 or oute1 and oute2 (I don't see oute in the manual).
Forum: Bioinformatics 12-11-2016, 04:15 AM
Replies: 665
Views: 151,056
Posted By moistplus
Can you confirm that pileup doesn't need sam...

Can you confirm that pileup doesn't need sam files to be sorted ?
Forum: Bioinformatics 12-02-2016, 01:17 PM
Replies: 34
Views: 115,275
Posted By moistplus
Yes it's PCR amplified.

Yes it's PCR amplified.
Forum: Bioinformatics 12-02-2016, 11:42 AM
Replies: 34
Views: 115,275
Posted By moistplus
PCR duplicatas are just redundant informations so...

PCR duplicatas are just redundant informations so removing it will not afftect the final quality of the assembly I guess ?
Forum: Bioinformatics 12-01-2016, 02:07 AM
Replies: 128
Views: 52,997
Posted By moistplus
Is that possible to output the 2 fastq and a sam...

Is that possible to output the 2 fastq and a sam file at the same time ?
Forum: Bioinformatics 11-29-2016, 02:13 AM
Replies: 665
Views: 151,056
Posted By moistplus
cat is working ? because there are the headers...

cat is working ? because there are the headers (@).

pileup does not take account of that ?
Forum: Bioinformatics 11-28-2016, 01:25 PM
Replies: 665
Views: 151,056
Posted By moistplus
In the case where I have 2 libraries (or more);...

In the case where I have 2 libraries (or more); for instance one paired end and one single; so the commands would be:



and



Then I merge the 2 bam files with
Forum: Bioinformatics 11-28-2016, 12:09 PM
Replies: 665
Views: 151,056
Posted By moistplus
I would like to map my reads to my draft assembly...

I would like to map my reads to my draft assembly to compute the coverage.
Forum: Bioinformatics 11-28-2016, 06:29 AM
Replies: 665
Views: 151,056
Posted By moistplus
what is the default number of mismatch and how...

what is the default number of mismatch and how can I change it ?
Forum: Bioinformatics 11-23-2016, 12:46 PM
Replies: 128
Views: 52,997
Posted By moistplus
Your tool is amazing ! there are everythings ! ...

Your tool is amazing ! there are everythings !

If I set outm=normal_pairs.fq , I will have interleaved paired end ?
Forum: Bioinformatics 11-23-2016, 11:39 AM
Replies: 128
Views: 52,997
Posted By moistplus
Thanks Genomax. So if I undertand well, I...

Thanks Genomax.
So if I undertand well, I should set killbadpairs and pairedonly to true ?
Forum: Bioinformatics 11-23-2016, 11:31 AM
Replies: 665
Views: 151,056
Posted By moistplus
Hi Brian, I have created an index with ...

Hi Brian,

I have created an index with



1) I would like to map my paired end reads and extract the paired end that have mapped to my genome.
I am not sure about the command.

Is it ?
Forum: Bioinformatics 11-23-2016, 10:50 AM
Replies: 128
Views: 52,997
Posted By moistplus
In fact I would like to estimate my insert size...

In fact I would like to estimate my insert size and the orientation also.

I have ran the classical bwa mem and picard tools CollectInsertSizeMetrics after an assembly.

For some lib, I see...
Forum: Bioinformatics 11-22-2016, 11:37 AM
Replies: 128
Views: 52,997
Posted By moistplus
Thank you, I'm gonna try it. What is the...

Thank you, I'm gonna try it.

What is the equivalent option to bwa mem -M (for single mapping) ?
Forum: Bioinformatics 11-22-2016, 05:16 AM
Replies: 128
Views: 52,997
Posted By moistplus
is it possible to estimate insert size of non...

is it possible to estimate insert size of non overlapped library ?
Forum: Bioinformatics 11-16-2016, 01:35 AM
Replies: 219
Views: 69,332
Posted By moistplus
Can you confirm that sampling reads is random ? ...

Can you confirm that sampling reads is random ?

reformat.sh in1=reads1.fq in2=reads2.fq out1=sampled1.fq out2=sampled2.fq samplerate=0.1
Forum: Bioinformatics 11-15-2016, 06:14 AM
Replies: 34
Views: 115,275
Posted By moistplus
Do you think it could be useful to remove those...

Do you think it could be useful to remove those duplicates (with Picard tools MarkDuplicates) for a de novo genome assembly ?
Forum: Bioinformatics 11-10-2016, 05:57 AM
Replies: 3
Views: 2,122
Posted By moistplus
Do you have some source that Miseq has lower...

Do you have some source that Miseq has lower error rate that Hiseq ?
Forum: Bioinformatics 11-09-2016, 01:46 AM
Replies: 219
Views: 69,332
Posted By moistplus
With the new version, I don't have anymore...

With the new version, I don't have anymore negative coverage!

Another question:
Using this command :



in1 and in2 are Forward reads and Reverse reads right ? So it keeps the mated pair at...
Forum: Bioinformatics 11-08-2016, 01:34 AM
Replies: 219
Views: 69,332
Posted By moistplus
1) So I have PE from 2 differents library: PE...

1) So I have PE from 2 differents library:
PE 350 (insert size)
PE 550

I merged them with a simple cat so I have at the end F reads (pair1) and R reads (pair2).

2) Mapping with bwa:

bwa...
Forum: Bioinformatics 11-07-2016, 05:47 AM
Replies: 219
Views: 69,332
Posted By moistplus
I've ran pileup for contig coverage estimation...

I've ran pileup for contig coverage estimation after assembly.

The output is :

ID Avg_fold Length Ref_GC Base_Coverage Read_GC

1) The coverage is the Avg_fold right ?

2) If yes, I have...
Forum: Bioinformatics 08-30-2016, 02:37 AM
Replies: 665
Views: 151,056
Posted By moistplus
Hi, Do you have a tool to compute insert...

Hi,

Do you have a tool to compute insert size from a .bam file ?
I'm looking for statistics about orientation of my paired end or mate pair (RF, FR,...) and insert size corresponding to it.
Forum: Pacific Biosciences 08-15-2016, 04:01 AM
Replies: 3
Views: 3,378
Posted By moistplus
What is Q50 ?

What is Q50 ?
Forum: Bioinformatics 07-22-2016, 05:36 AM
Replies: 219
Views: 69,332
Posted By moistplus
Is it possible to compute the insert size (and...

Is it possible to compute the insert size (and make a histogram distribution) from a .bam file ?
Showing results 1 to 25 of 40

 


All times are GMT -8. The time now is 12:54 PM.


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