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Forum: De novo discovery 03-07-2014, 09:33 AM
Replies: 37
Views: 20,146
Posted By MeganS
sabiha, Does the stdout from bank-transact...

sabiha,

Does the stdout from bank-transact report any "Objects added"?

Are your .xml files links of some sort (paired reads, etc)? I have gotten bambus to work, but used the .xml link...
Forum: Bioinformatics 08-13-2013, 09:27 AM
Replies: 1
Views: 2,266
Posted By MeganS
What type of samples are these(whole genome,...

What type of samples are these(whole genome, transcriptome, RAD, etc.)? It could be contamination of some sort. You can tile the kmers together to get a longer sequence (TATCCTCCAGTG). I would...
Forum: Bioinformatics 04-23-2013, 10:17 PM
Replies: 4
Views: 4,440
Posted By MeganS
Estimating heterozygosity from kmer frequency distribution

Is there a program that can estimate the heterozygosity of a sample using the kmer frequency distribution of the raw reads? I have whole genome, Illumina data (100bp PE reads, from 300bp fragments)....
Forum: Bioinformatics 04-15-2013, 08:33 AM
Replies: 2
Views: 1,067
Posted By MeganS
MAKER comes with an accessory script...

MAKER comes with an accessory script (maker_functional_fasta) that maps functional information onto a fasta. It might take some shuffling of your BLAST output to get it in the expected input format....
Forum: Bioinformatics 03-27-2013, 10:31 PM
Replies: 3
Views: 2,635
Posted By MeganS
Here are a couple posts/blogs with some...

Here are a couple posts/blogs with some references included:

http://seqanswers.com/forums/showthread.php?t=11843
...
Forum: Bioinformatics 03-21-2013, 12:58 PM
Replies: 7
Views: 6,362
Posted By MeganS
Merge the overlapping reads. There are a number...

Merge the overlapping reads. There are a number of tools that do this (eg FLASH)
Forum: Bioinformatics 03-20-2013, 09:20 AM
Replies: 3
Views: 2,635
Posted By MeganS
1) I think removing the adapters is probably...

1) I think removing the adapters is probably better. Check the BWA documentation, but I think it treats Ns as a mismatch to the reference.
2) I trim 6 bases off the 5' end of RNA-seq (due to a...
Forum: General 03-03-2013, 09:07 AM
Replies: 7
Views: 10,193
Posted By MeganS
xhuister, check your read lengths. That is what...

xhuister, check your read lengths. That is what the error message seems to be indicating. You could also try entering the flowcell as "Illumina:@HWUSI-EAS1571_0012". That is the format I used and...
Forum: RNA Sequencing 02-13-2013, 03:06 PM
Replies: 1
Views: 2,117
Posted By MeganS
You can use "samtools view" to pull out the...

You can use "samtools view" to pull out the region of interest (in sam/bam format) and "picard SamToFastq.jar" to pull out the reads from the sam/bam (in fastq format).
Forum: RNA Sequencing 01-14-2013, 03:57 PM
Replies: 9
Views: 6,219
Posted By MeganS
I have been using trimmomatic for exactly the...

I have been using trimmomatic for exactly the same situation and I have been happy with the results. Here is the command I am using:

java -classpath <path_trimmomatic>...
Forum: Bioinformatics 01-08-2013, 09:38 AM
Replies: 2
Views: 1,572
Posted By MeganS
There are a number of annotation pipelines...

There are a number of annotation pipelines available. MAKER would probably be a good place to start (http://gmod.org/wiki/MAKER)
Forum: Bioinformatics 12-08-2012, 11:14 AM
Replies: 0
Views: 1,144
Posted By MeganS
Trimmomatic palindrome clipping (MIN_PREFIX=8)

I have Illumina RNA-Seq data with extremely short fragment sizes (150bp for 100bpPE reads). I am using Trimmomatic because I like how the palindrome clipping handles read-through (and bonus points...
Forum: Bioinformatics 12-08-2012, 10:53 AM
Replies: 2
Views: 1,088
Posted By MeganS
I think this is likely an issue during sequencing...

I think this is likely an issue during sequencing rather than library prep. We see a similar thing occasionally and when it occurs it is always seen in all samples that were run together in a lane,...
Forum: Bioinformatics 01-12-2012, 06:43 PM
Replies: 5
Views: 2,932
Posted By MeganS
why retain unmapped reads?

I have heard that it is important for downstream analyses to retain unmapped reads. I am interested to know the reason for this recommendation.

Specifically, I am using BWA + GATK to call SNPs...
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