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Search took 0.00 seconds. Search: Posts Made By: jbrwn
Forum: Bioinformatics 10-10-2012, 09:11 AM
Replies: 6
Views: 4,654
Posted By jbrwn
diffbind was suggested because if you were to use...

diffbind was suggested because if you were to use something like macs to call peaks, it would not take biological replicates into consideration. after calling peaks in macs, you would use diffbind to...
Forum: Bioinformatics 10-09-2012, 03:26 PM
Replies: 6
Views: 4,289
Posted By jbrwn
uses a good amount of memory since it's storing...

uses a good amount of memory since it's storing one fq in a dict, but seems to work:

https://gist.github.com/3861828

edit: you didn't say anything about preserving the quals, so this prints a...
Forum: Bioinformatics 10-09-2012, 02:20 PM
Replies: 9
Views: 6,912
Posted By jbrwn
honestly, that seems about right. bowtie2 made...

honestly, that seems about right. bowtie2 made improvements to paired-end, so you may want to check that out. paired-end specific options:...
Forum: Bioinformatics 10-08-2012, 09:17 AM
Replies: 6
Views: 4,289
Posted By jbrwn
do you know how to use the command line at all?...

do you know how to use the command line at all? post the first read name from each fastq and i'll try to help you out. my solution will require python.
Forum: Bioinformatics 08-16-2012, 02:22 PM
Replies: 13
Views: 4,203
Posted By jbrwn
in rum, you can preserve read names using...

in rum, you can preserve read names using ``--preserve-names`` (where all reads are the same length).

i wish they all had the equivalent to ``bowtie -m1``.
Forum: RNA Sequencing 02-08-2012, 11:40 AM
Replies: 13
Views: 4,815
Posted By jbrwn
bummer. for exon counting i have reverted to...

bummer.

for exon counting i have reverted to using there supplied script within the dexseq package (dexseq_count.py) which depends on htseq.

i assume you already have the package and used one...
Forum: Bioinformatics 02-08-2012, 10:45 AM
Replies: 4
Views: 1,788
Posted By jbrwn
the only online tool i rely on is the ucsc...

the only online tool i rely on is the ucsc browser and it works under Chrome.
Forum: RNA Sequencing 02-08-2012, 10:20 AM
Replies: 13
Views: 4,815
Posted By jbrwn
the script doesn't like that you don't have a...

the script doesn't like that you don't have a dash (-) before the "i".
Forum: Bioinformatics 02-01-2012, 09:45 AM
Replies: 4
Views: 4,129
Posted By jbrwn
can't you skip the awk pipe by adjusting your...

can't you skip the awk pipe by adjusting your samtools view with:
samtools view -SbF 4 -
Forum: Bioinformatics 01-31-2012, 10:08 AM
Replies: 2
Views: 1,784
Posted By jbrwn
there may be problems in other areas, but it's...

there may be problems in other areas, but it's difficult to troubleshoot with the given information. things that would help are fragment and read length, whether the reads are actually paired-end or...
Forum: Bioinformatics 01-31-2012, 09:44 AM
Replies: 3
Views: 2,050
Posted By jbrwn
i typically include --mate-std-dev <int> as well,...

i typically include --mate-std-dev <int> as well, though i'm not sure how much difference it makes. this information should be available from the bioanalyzer output or someone-from-the-lab output.
Forum: Bioinformatics 01-31-2012, 09:40 AM
Replies: 3
Views: 2,050
Posted By jbrwn
a space between file_1 and file_2.

a space between file_1 and file_2.
Forum: Bioinformatics 01-30-2012, 03:22 PM
Replies: 4
Views: 5,212
Posted By jbrwn
map them all as individuals in tophat, then use...

map them all as individuals in tophat, then use samtools merge to put them together.
Forum: RNA Sequencing 01-13-2012, 12:36 PM
Replies: 11
Views: 7,297
Posted By jbrwn
it's a good point, but this thread was to answer...

it's a good point, but this thread was to answer the original poster's question about single end reads.
Forum: Bioinformatics 01-02-2012, 10:54 AM
Replies: 23
Views: 16,943
Posted By jbrwn
what's the location of gtf_to_sam? what's your...

what's the location of gtf_to_sam? what's your $PATH? did you source your bashrc or log out and back in?
Forum: Bioinformatics 12-28-2011, 09:52 AM
Replies: 32
Views: 35,094
Posted By jbrwn
it's definitely not very rigorous. htseq has a...

it's definitely not very rigorous. htseq has a fastq reader in it which could help you subsample randomly.
htseq tour (http://www-huber.embl.de/users/anders/HTSeq/doc/tour.html)
previous discussion...
Forum: Bioinformatics 12-27-2011, 08:41 PM
Replies: 4
Views: 2,361
Posted By jbrwn
rather than that perl, pipe it into this: awk...

rather than that perl, pipe it into this:
awk 'BEGIN{OFS=FS="\t"}/^@/{print}!/^@/{if(length($10)==30) print}'
it'll print the header and any line where the sequence (column 10) is 30 characters.
Forum: Bioinformatics 12-27-2011, 09:50 AM
Replies: 21
Views: 40,473
Posted By jbrwn
No need to worry about either of these. The...

No need to worry about either of these. The second line concerning the bam would make more sense if you posted the next line of the output which is something like, "Trying SAM", which does work....
Forum: RNA Sequencing 12-21-2011, 06:03 PM
Replies: 11
Views: 7,297
Posted By jbrwn
you're right about each read having a unique...

you're right about each read having a unique name, but reads with the same id will sometimes map multiple times. thus, giving you multiple entries in the bam with the same read name.
Forum: RNA Sequencing 12-21-2011, 05:20 PM
Replies: 11
Views: 7,297
Posted By jbrwn
right, and for total reads counts the lines of...

right, and for total reads counts the lines of your fastq and divide by 4.
Forum: Bioinformatics 12-21-2011, 04:51 PM
Replies: 2
Views: 3,132
Posted By jbrwn
grab header samtools view -H .bam > new.sam ...

grab header
samtools view -H .bam > new.sam
stick on the unique reads
samtools view .bam | grep ... >> new.sam
convert to bam
samtools view -Sb -o unique.bam new.sam

also check out samtools...
Forum: Bioinformatics 11-11-2011, 09:12 AM
Replies: 21
Views: 10,933
Posted By jbrwn
after re-reading some of perl scripts i lost hope...

after re-reading some of perl scripts i lost hope for it and switched to python. i started with this:
Learn Python The Hard Way (http://learnpythonthehardway.org/book/)
Forum: Bioinformatics 11-10-2011, 09:04 PM
Replies: 2
Views: 2,055
Posted By jbrwn
what nicolas said. use cuffmerge to merge the two...

what nicolas said. use cuffmerge to merge the two *.gtf files from cufflinks output.
Forum: Bioinformatics 11-09-2011, 02:30 PM
Replies: 9
Views: 5,674
Posted By jbrwn
in addition to posting your reference, you may...

in addition to posting your reference, you may want to post which options you're utilizing in cufflinks.
Forum: Bioinformatics 11-09-2011, 02:21 PM
Replies: 6
Views: 1,752
Posted By jbrwn
to get everything just: samtools view .bam ...

to get everything just:
samtools view .bam

to get everything and the header:
samtools view -h .bam

for .sam, add the sam option
samtools view -S .sam

however, if you did want to make...
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