SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 25 of 91
Search took 0.01 seconds.
Search: Posts Made By: winsettz
Forum: Bioinformatics 12-23-2013, 12:13 AM
Replies: 4
Views: 2,669
Posted By winsettz
0.75 or 0.75a? Also, bwa sampe or bwa mem?

0.75 or 0.75a?

Also, bwa sampe or bwa mem?
Forum: Bioinformatics 10-28-2013, 07:42 AM
Replies: 9
Views: 4,242
Posted By winsettz
You should be able to extract that information...

You should be able to extract that information from the sam output. I've not used bowtie2-inspect before, but it could be what you are looking for.


bowtie2-inspect
No index name given!
Bowtie...
Forum: Bioinformatics 10-28-2013, 07:37 AM
Replies: 5
Views: 2,360
Posted By winsettz
Also, the "reverse complement" stuff comes from...

Also, the "reverse complement" stuff comes from the illumina nextera application note. The note is "Current as of 17 December 2012" (Pub. No 770-2012-053).
Forum: Bioinformatics 10-28-2013, 06:29 AM
Replies: 5
Views: 2,360
Posted By winsettz
I've /heard/ that velvet required...

I've /heard/ that velvet required reverse-complementing; but generally if an assembler has explicit flags to set mate-pair libraries, it should generally be able to handle them properly without...
Forum: Bioinformatics 10-25-2013, 02:00 PM
Replies: 10
Views: 19,073
Posted By winsettz
An example of my shell script that I use to kick...

An example of my shell script that I use to kick off Trimmomatic jobs (derived from Trimmomatic-0.30.zip)
ADAPTER=TruSeq3
ORIENTATION=PE #or SE
java -jar...
Forum: General 10-25-2013, 01:26 PM
Replies: 0
Views: 1,611
Posted By winsettz
Forum-related: name changes?

Thinking of changing forum name. Is this possible?
Forum: Bioinformatics 10-25-2013, 01:18 PM
Replies: 3
Views: 924
Posted By winsettz
This /should/ work. Post the rest of the error...

This /should/ work. Post the rest of the error message.

bowtie2 -p 8 -x hg19 -f -U ~/my_rnaseq_dat/untreated1.fa -S untreated.sam
Forum: Bioinformatics 10-25-2013, 11:37 AM
Replies: 6
Views: 4,390
Posted By winsettz
Indeed, my code is update_blastdb.pl nt ...

Indeed, my code is

update_blastdb.pl nt
for N in {00..13}; do tar zxvpf nr.$N.tar.gz; done
blastp -db nr


Getting

blastp -db nr
Forum: Bioinformatics 10-25-2013, 10:13 AM
Replies: 6
Views: 4,390
Posted By winsettz
How silly of me. Thought nr was non redundant...

How silly of me. Thought nr was non redundant nucleotide. I will test soon.

Any thoughts on the blastdbcheck messages?
Forum: Bioinformatics 10-25-2013, 08:51 AM
Replies: 3
Views: 924
Posted By winsettz
Pretty sure it's supposed to be U. I thought...

Pretty sure it's supposed to be U. I thought flags are case sensitive.
Forum: Bioinformatics 10-25-2013, 07:16 AM
Replies: 6
Views: 4,390
Posted By winsettz
Deploying a local version of blast, having issues

Compiling ncbi-blast itself appears to have gone fine. Where I have issues with is multi-partite blast databases. The error messages are worrying, but maybe it's not a big deal after all?

For...
Forum: Bioinformatics 10-24-2013, 10:33 AM
Replies: 7
Views: 1,534
Posted By winsettz
I suppose if you had the original samples, the...

I suppose if you had the original samples, the experimental way to do it would be quantitative PCR. With reads, you could probably determine nucleotide coverage of your Mycoplasma marker, or ideally,...
Forum: Bioinformatics 10-24-2013, 09:41 AM
Replies: 10
Views: 4,901
Posted By winsettz
There's an hgPcr in the lastest copy of...

There's an hgPcr in the lastest copy of jksrc.zip. I've yet to to look into the code yet to determine if it's the same as the hgPcr in silico PCR on the website.

Edit: Or you can go to
...
Forum: Bioinformatics 10-24-2013, 09:22 AM
Replies: 7
Views: 1,534
Posted By winsettz
If I remember correctly, in the lab the way to do...

If I remember correctly, in the lab the way to do it is by PCR. In silico, you could recapitulate that by finding the gene that is PCR'ed and screen your reads for it. Can't say what the FP/FN rate...
Forum: Bioinformatics 10-21-2013, 08:42 AM
Replies: 1
Views: 1,424
Posted By winsettz
BLAST output already is fairly visual. Below is a...

BLAST output already is fairly visual. Below is a blastx result of mine.


Query= NODE_2_length_91_cov_18.516483

Length=181
...
Forum: Bioinformatics 10-18-2013, 10:58 AM
Replies: 8
Views: 2,087
Posted By winsettz
Chromosome location and orientation is what you...

Chromosome location and orientation is what you get from SAM/BAM.

If you have any questions; don't forget seqanswers has an RNAseq forum!
Forum: Bioinformatics 10-18-2013, 09:41 AM
Replies: 8
Views: 2,087
Posted By winsettz
Are you loading a reference fasta along with the...

Are you loading a reference fasta along with the SAM/bam file? Tablet has options to load both.

Didn't realize you could load the bai instead of the original fasta.

Edit: Converted a SAM+FASTA...
Forum: Bioinformatics 10-17-2013, 11:31 AM
Replies: 3
Views: 4,953
Posted By winsettz
Innie and outie refer to the orientation of the...

Innie and outie refer to the orientation of the reads. In standard paired end, the DNA is sheared and read from 5' to 3' of each strand. Since 5' is outside on both strands, the direction of the...
Forum: Sample Prep / Library Generation 10-16-2013, 01:45 PM
Replies: 2
Views: 4,163
Posted By winsettz
This is the first I've heard of MALBAC. However,...

This is the first I've heard of MALBAC. However, there are some MALBAC reads (Human Sperm Genome Sequencing at Harvard) in the SRA that may yield insights into the nature of MALBAC.
...
Forum: Bioinformatics 10-15-2013, 12:52 PM
Replies: 3
Views: 6,179
Posted By winsettz
[m@f ~]$ head 1 1 [m@f ~]$ head 2 2 [m@f...

[m@f ~]$ head 1
1
[m@f ~]$ head 2
2
[m@f ~]$ head 3
3
[m@f ~]$ cat 1 2 3 | head
1
2
3
Forum: Bioinformatics 10-15-2013, 12:32 PM
Replies: 3
Views: 4,953
Posted By winsettz
All the annotations are indeed with respect to...

All the annotations are indeed with respect to the read in question.

However, knowing something about the mate can be important. For instance, if you have a pair of reads with one read mapped and...
Forum: Bioinformatics 10-15-2013, 12:26 PM
Replies: 8
Views: 23,393
Posted By winsettz
Looks like fastqc will use one thread per file....

Looks like fastqc will use one thread per file. Reading the -help for fastqc it states --threads "Specifies the number of files which can be processed simultaneously". Perhaps upping --threads to...
Forum: Bioinformatics 10-12-2013, 05:47 PM
Replies: 3
Views: 6,695
Posted By winsettz
I would assume that having four different insert...

I would assume that having four different insert sizes would suggest four different libraries. I guess he didn't say how much memory his job is taking, "bigmem" is vague. Velvet's also pretty...
Forum: Bioinformatics 10-12-2013, 11:50 AM
Replies: 3
Views: 6,695
Posted By winsettz
Depending on the size of your files, might...

Depending on the size of your files, might compiling with BIGASSEMBLY be required? Not sure if that'll solve your problem. Have you tried running the assembly with the shorter paired end libraries...
Forum: General 10-09-2013, 09:33 AM
Replies: 4
Views: 5,223
Posted By winsettz
I /was/ a double-majored...

I /was/ a double-majored microbiology/biochemistry major, worked in analytical chemistry and did research in a biochemistry lab when I went into graduate school for computational biology. It's...
Showing results 1 to 25 of 91

 


All times are GMT -8. The time now is 03:13 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO