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Forum: Bioinformatics 03-23-2012, 01:55 AM
Replies: 12
Views: 6,024
Posted By epigen
That is more or less what I did before using the...

That is more or less what I did before using the new Picard tool. The -r option will automatically create the RG tag for each read, the name is inferred from the BAM file name so that in the example...
Forum: Bioinformatics 03-22-2012, 10:57 AM
Replies: 12
Views: 6,024
Posted By epigen
You need a @RG line in the header for each single...

You need a @RG line in the header for each single BAM file to merge then with Picard. You can supply it to bwa sampe as an option. If you missed to do that, there is now a Picard tool "add or replace...
Forum: Bioinformatics 09-19-2011, 03:33 AM
Replies: 35
Views: 20,867
Posted By epigen
Hi guo, making Bioscope run gives even...

Hi guo,

making Bioscope run gives even system administrators a hard time. (Ours complained a lot ...) When you installed it, did you tell it you have 128 nodes? It's better to reduce the number...
Forum: SOLiD 08-15-2011, 10:58 AM
Replies: 26
Views: 14,384
Posted By epigen
Is it really that long ago already? I haven't...

Is it really that long ago already? I haven't been around the forum for some months now due to a very high workload. We're struggling with 50+35 bp PE tumor + matched control samples. I didn't test...
Forum: Bioinformatics 05-20-2011, 07:15 AM
Replies: 29
Views: 13,202
Posted By epigen
identify breakpoints with softclipped reads

That's a very good question. Maybe softclipped reads don't give enough evidence?
Forum: SOLiD 03-21-2011, 09:45 AM
Replies: 13
Views: 3,418
Posted By epigen
For BWA, you'd have to strip the T, convert 0 to...

For BWA, you'd have to strip the T, convert 0 to A, 1 to C, 2 to G, 3 to T and anything else to N. That's pseudo-nucleotide representation of color space, which was introduced as a workaround. It has...
Forum: Bioinformatics 03-17-2011, 08:43 AM
Replies: 2
Views: 2,865
Posted By epigen
That has been noticed before, see here: ...

That has been noticed before, see here:
[Bio-bwa-help] Repetitive reads are not randomly placed...
Forum: Bioinformatics 03-17-2011, 08:06 AM
Replies: 2
Views: 2,773
Posted By epigen
The BFAST developers recommend to use bfast...

The BFAST developers recommend to use bfast bwaaln for 25 (35) bp reads. But 25+25 bp is really really short, I thought the mate-pair standard is 50+50 whereas for paired-end it's 50+35 (I work with...
Forum: Bioinformatics 03-17-2011, 07:56 AM
Replies: 2
Views: 2,125
Posted By epigen
1) SNP callers are generally designed for diploid...

1) SNP callers are generally designed for diploid organisms, check if there is an explicit option for haploid ones.
2) Different parameters (cutoff for mapping quality, base quality, coverage,...
Forum: Bioinformatics 03-17-2011, 07:16 AM
Replies: 3
Views: 1,512
Posted By epigen
If your alignment is in BAM format, samtools...

If your alignment is in BAM format, samtools mpileup and bcftools is likely the best choice:
http://samtools.sourceforge.net/mpileup.shtml
You can get SNPs and Indels in vcf format for each...
Forum: Bioinformatics 03-17-2011, 07:07 AM
Replies: 31
Views: 12,526
Posted By epigen
I also split the short reads for bwaaln, then...

I also split the short reads for bwaaln, then feed the resulting shortreads.<nr>.bmf file and the longreads.<nr>.bmf from match into localalign, like that:
bfast localalign -f $REF -1...
Forum: Bioinformatics 03-01-2011, 10:35 AM
Replies: 29
Views: 13,202
Posted By epigen
get discordant pairs

If you extract the discordant pairs from your BAM file like that:

samtools view -hb -F 1038 orig.bam > discordant.bam

you get reads that have neither flag 2 (proper pair) nor flag 4 (read...
Forum: Bioinformatics 03-01-2011, 06:51 AM
Replies: 8
Views: 2,231
Posted By epigen
convert Illumina scores to Phred in a BAM file

If you already have a BAM file, you can transform the scores in it as follows:

samtools view -h Illumina_score.bam | perl -lane '$"="\t"; if (/^@/) {print;} else {$F[10]=~...
Forum: Bioinformatics 03-01-2011, 06:47 AM
Replies: 11
Views: 7,200
Posted By epigen
convert Illumina scores into Phred scores in a BAM file

Although this thread is quite old, I found it extremely useful. Thanks for providing the efficient way to convert Illumina scores into Phred scores, rmdavies!
I used it to transform the scores in a...
Forum: Bioinformatics 02-24-2011, 08:50 AM
Replies: 1
Views: 2,045
Posted By epigen
MACS does not use any quality filters and if a...

MACS does not use any quality filters and if a read is mapped to different locations it will count it just as many times. It only removes reads that it considers to be duplicates (same start...
Forum: Bioinformatics 02-15-2011, 07:47 AM
Replies: 4
Views: 11,981
Posted By epigen
If you mean Heng Li's software, they are part of...

If you mean Heng Li's software, they are part of the latest samtools distribution, see
http://samtools.sourceforge.net/
Forum: Bioinformatics 02-15-2011, 05:48 AM
Replies: 2
Views: 6,394
Posted By epigen
Bedtools intersectBed with vcf format

Since I could not find any documentation on how Bedtools intersectBed works with vcf format, I'm posting my question here:

I'm intersecting a vcf file from mpileup and bcftools with dbSNP132 that...
Forum: Bioinformatics 02-15-2011, 05:04 AM
Replies: 5
Views: 1,722
Posted By epigen
The length of your peaks depends on the value for...

The length of your peaks depends on the value for the --bw parameter you give MACS. It should be the same as the fragment size. The higher the value, the longer the peaks.
Forum: Bioinformatics 02-04-2011, 06:14 AM
Replies: 2
Views: 4,093
Posted By epigen
The tools you're using just report the SNPs found...

The tools you're using just report the SNPs found in your data. You'll have to assign the SNPs the dbSNP data with another tool, e.g. GATK VariantAnnotator, to which you provide the dbSNP entries as...
Forum: Bioinformatics 01-19-2011, 03:03 AM
Replies: 12
Views: 6,024
Posted By epigen
BioScope produced bam files have RG information...

BioScope produced bam files have RG information in the header and Picard keeps it there. I don't know what samtools does, it might ignore it unless you use the -r and -h options (which will change...
Forum: Bioinformatics 01-19-2011, 02:50 AM
Replies: 9
Views: 12,039
Posted By epigen
candidates not allele-specific

Finally we got the results from the validation of our candidates - and a big disappointment: almost all turned out to be expressed perfectly 50:50 instead of allele-specific!
Since in some papers...
Forum: Bioinformatics 01-13-2011, 05:04 AM
Replies: 1
Views: 2,679
Posted By epigen
Have you found out what went wrong? It seems...

Have you found out what went wrong?
It seems the pairs were matched correctly because the number of singletons increased drastically:
before:
287049 with itself and mate mapped
44298 singletons...
Forum: Bioinformatics 01-04-2011, 06:42 AM
Replies: 20
Views: 18,357
Posted By epigen
If your reference sequence is correct and...

If your reference sequence is correct and indexed, as well as you BAM file, you should see the reference sequence where reads aligned. I noted that if there are no reads for a long stretch of bases,...
Forum: Bioinformatics 01-04-2011, 06:26 AM
Replies: 2
Views: 2,293
Posted By epigen
What version are you using? I copied your...

What version are you using? I copied your examples and it worked with v2.10.0:

chr1 bed2gff exon 4541 4636 0.0 * . gene_id "chr1:4540-4636"; transcript_id "chr1:4540-4636"; exon_number...
Forum: Bioinformatics 01-04-2011, 06:04 AM
Replies: 12
Views: 6,024
Posted By epigen
Thank you again. I'll use samtools merge and try...

Thank you again. I'll use samtools merge and try if Picard works with the RG tag. (If not, I'll go through the BAM file and add unique read names and RG.) For future BFAST aligments I'll surely use...
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