Forum: Bioinformatics
05-08-2013, 11:50 AM
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Replies: 2
Views: 89
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Forum: Bioinformatics
05-08-2013, 08:21 AM
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Replies: 2
Views: 89
wildcard use for bowtie2 unpaired read sets?
Hi all (and specifically @salzberg),
I've been trying to figure out a way to map a batch of unpaired fastq.gz files in the bowtie2 command line without manually entering a comma separated list of...
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Forum: Bioinformatics
05-07-2013, 10:30 AM
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Replies: 8
Views: 152
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Forum: Bioinformatics
05-07-2013, 10:27 AM
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Replies: 8
Views: 152
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Forum: Bioinformatics
05-07-2013, 10:21 AM
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Replies: 8
Views: 152
I thought about FastQC, but all really want is...
I thought about FastQC, but all really want is Number of Reads and base count or average read length...FastQC does a lot more (which is great) at the cost of time.
It may be my best alternative...
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Forum: Bioinformatics
05-07-2013, 09:34 AM
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Replies: 8
Views: 152
fastq.gz stats READ-COUNT BASE-COUNT
Hi all,
Before I try writing some inefficient code, I was wondering if anyone has a script to count read number and total base count (or average read length) from a gzipped fastq file or even...
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Forum: Bioinformatics
05-03-2013, 11:25 AM
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Replies: 2
Views: 182
For the KMER and GC plots, things start to...
For the KMER and GC plots, things start to normalize around 10 bp you may want to trim the 1st 10 bp.
As a rule of thumb I usually do the following QC and THEN run my data through FastQC:
(1)...
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Forum: Bioinformatics
05-01-2013, 08:28 AM
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Replies: 16
Views: 360
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Forum: Bioinformatics
05-01-2013, 08:13 AM
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Replies: 16
Views: 360
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Forum: Bioinformatics
05-01-2013, 07:59 AM
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Replies: 16
Views: 360
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Forum: Bioinformatics
05-01-2013, 07:58 AM
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Replies: 16
Views: 360
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Forum: Bioinformatics
04-24-2013, 06:05 AM
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Replies: 3
Views: 206
@ExMachina I would much rather have very few...
@ExMachina I would much rather have very few false positives even at the cost of losing true positives. I'm trying to get a reliable subset of single copy genes to calculate some statistics with....
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Forum: Bioinformatics
04-23-2013, 08:13 AM
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Replies: 3
Views: 206
Identifying Single Copy Human Genes
Hi all,
I am trying to come up with a conservative list of single copy human genes -- i.e. I want to exclude all genes that may be part of a larger gene family/have highly similar sequence...
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Forum: Illumina/Solexa
04-17-2013, 01:28 PM
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Replies: 4
Views: 243
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Forum: Bioinformatics
04-03-2013, 09:10 AM
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Replies: 9
Views: 297
For anyone still interested...
For...
For anyone still interested...
For simplicity, I ended up using Bioawk (https://github.com/lh3/bioawk):
Get the mean Phred quality score from FASTQ:
awk -c fastx '{ print ">"$name; print...
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Forum: Bioinformatics
03-25-2013, 10:55 AM
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Replies: 9
Views: 297
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Forum: Bioinformatics
03-25-2013, 08:14 AM
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Replies: 9
Views: 297
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Forum: Bioinformatics
03-25-2013, 07:28 AM
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Replies: 9
Views: 297
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Forum: Bioinformatics
03-25-2013, 05:32 AM
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Replies: 9
Views: 297
average quality score for fastq file
Hello,
Simple question here, but I've had a problem finding a program to do it.
Given a fastq file, is there software that will calculate the average quality score for the entire file?
Thanks
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Forum: Bioinformatics
03-21-2013, 01:02 PM
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Replies: 6
Views: 356
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Forum: RNA Sequencing
03-20-2013, 06:46 AM
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Replies: 3
Views: 360
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Forum: Bioinformatics
03-19-2013, 09:08 AM
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Replies: 12
Views: 392
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Forum: Introductions
03-19-2013, 06:18 AM
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Replies: 2
Views: 678
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Forum: Bioinformatics
03-19-2013, 06:13 AM
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Replies: 12
Views: 392
Hi Maria,
Sorry -- I meant to reply earlier....
Hi Maria,
Sorry -- I meant to reply earlier. Yes, the script works fine just with the command line perl statement. Luckily, I am not doing this on the whole genome scale. In brief, I'm intereste din...
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Forum: Bioinformatics
03-18-2013, 09:03 AM
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Replies: 12
Views: 392
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