User: finswimmer
finswimmer • 280
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Posts by finswimmer
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1
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1
answer
168
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... Hello,
what was the exact command you use for Picards AddOrReplaceReadGroups? Please also post the bam header. For this you can use this command:
samtools view -H /home/mahnoor/Documents/IGV_DATA/Wheat_DATA/reference.bam
fin swimmer ...
written 3 days ago by
finswimmer • 280
1
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5
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286
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5
answers
Comment:
C: Why not merging?
... Hello jomo018,
of course you're right, that in repeating region there is a chance of incorrect merging. But e.g. bbmerge [didn't merge reads][1] if it finds a repeated region in the overlap. Also choosing a large enough minimum overlap reduces the risk of a false merge, but give me the advantages o ...
written 3 days ago by
finswimmer • 280
0
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5
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286
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5
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Answer:
A: Why not merging?
... Hello all and thank you for your answers.
But I still see no great disadvantages if I merge overlapping reads :)
Ok, there is a risk that the merge is incorrect. But as Brian stated, it depends on the merger I use and what parameters I choose. So I can lower this risk to a point, where the advanta ...
written 4 days ago by
finswimmer • 280
19
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5
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9 follow
5
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... Hello,
I have a more general question. I do targeted, paired-end DNA resequencing. Before the alignment I merge overlapping read paires, which improves my variant outcome in that way, that I have much less artefacts or pseudogenvariants. I'm happy with it.
But it seems that most people doesn't mer ...
written 6 days ago by
finswimmer • 280
1
vote
1
answer
131
views
1
answers
Comment:
C: GATK: SNP coverage too high?
... From the HaplotypeCaller manual:
> The HaplotypeCaller is capable of calling SNPs and indels simultaneously via local de-novo assembly of haplotypes in an active region. In other words, whenever the program encounters a region showing signs of variation, it discards the existing mapping informat ...
written 13 days ago by
finswimmer • 280
0
votes
1
answer
131
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1
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Comment:
C: GATK: SNP coverage too high?
... Hello,
it's just a guess, but GATKs HaplotypeCaller is doing a [denovo assembly][1] around the region it suspects a variant. So I guess the 275 reads in the log file are the reads with which the assembly is done.
To see how GATK remap the reads you can follow this [how-to][2].
fin swimmer
[1]: ...
written 13 days ago by
finswimmer • 280
0
votes
2
answers
188
views
2
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Comment:
C: tabix for ID column
... Sorry for my late answer,
I didn't have the time to try it until now, but I will.
But I suspect the index file will be huge if it is uncrompressed.
fin swimmer ...
written 17 days ago by
finswimmer • 280
0
votes
2
answers
211
views
2
answers
Comment:
C: Help with finding introns
... Gateway Time-Out normaly means something take to long. Just retry it. I cannont reproduce it here this time, even if your linke still contains characters that should not be there (%0A).
Again the question: How do yoi create these urls?
fin swimmer ...
written 17 days ago by
finswimmer • 280
0
votes
2
answers
211
views
2
answers
Comment:
C: Help with finding introns
... > O.K. thanks. How can I ensure That it wont repet this error?
It depends on how you generate the url. Without knowing it, it is quite hard to help. ...
written 20 days ago by
finswimmer • 280
0
votes
2
answers
211
views
2
answers
Comment:
C: Help with finding introns
... Hello,
the error results from the %0D%0A in the url. %0D%0A encodes a line break. Remove it and it should work.
fin swimmer ...
written 20 days ago by
finswimmer • 280
Latest awards to finswimmer
Teacher
5 weeks ago,
created an answer with at least 3 up-votes.
For A: How to merge multiple bam files into single bam file
Scholar
6 weeks ago,
created an answer that has been accepted.
For A: How to merge multiple bam files into single bam file
Scholar
4 months ago,
created an answer that has been accepted.
For A: How to merge multiple bam files into single bam file
Teacher
4 months ago,
created an answer with at least 3 up-votes.
For A: How to merge multiple bam files into single bam file
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