User: lyfsa
lyfsa • 30
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Posts by lyfsa
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12
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3
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2.8k
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... Hi,
Please suggest me some tools which can detect large indels (esp. of size > 100bp). Some of the tools I have already tried include Breakdancer and Pindel and Hydra. Any other suggestions??
...
written 7.9 years ago by
lyfsa • 30
• updated
7.9 years ago by
zam.iqbal.genome • 1.7k
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... Hi There,
I am using trying to detect SV using Hydra-SV. I skip all the first 3 steps as described in the workflow as I used stampy for mapping which I assume is sensitive enough. So i extracted all the discordant read-pairs and use pairDiscordants.py and dedupDiscordants.py script. But when I use ...
written 7.9 years ago by
lyfsa • 30
• updated
7.9 years ago by
Istvan Albert ♦♦ 84k
0
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... I went through that link. But it looks like I cannot validate indels result from different caller??
...
written 7.9 years ago by
lyfsa • 30
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2.4k
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... After running the velvet and realigning them back to reference using mummer, I get several numbers of coordinates with 100% match with the ref sequence but I cannot make out long sequence out of that. I now have numbers of reads with many gaps in between. Can I say that if contig regions are overlap ...
written 7.9 years ago by
lyfsa • 30
0
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2.4k
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... Thank you..you information is of great help...
...
written 7.9 years ago by
lyfsa • 30
0
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2
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2.4k
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... Could you also tell me how velvet works for single end reads or unmapped reads in BAM files? I am quite skeptical about these reads.
...
written 7.9 years ago by
lyfsa • 30
3
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2
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2.4k
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2
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... Hi There,
I am trying to further verify indels detected from variant caller. For this, I extracted all the bam files reads, where indels were detected, run local assembly and realign the contigs from assembler back to reference to get the exact coordinates. My assumption is that, there should be g ...
written 7.9 years ago by
lyfsa • 30
• updated
7.9 years ago by
Jorge Amigo ♦ 11k
0
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1
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... Might be the case. How can I check for missing reads in two files? This is a first time I am using Illumina 1.8 reads for mapping. Before I used stampy with --bwaoption in illumina 1.3 reads and there was no error.
...
written 7.9 years ago by
lyfsa • 30
0
votes
1
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1.9k
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1
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... I have pair end reads from illumina 1.8 only. But as both illumina1.8 and sanger uses sanger format, Stampy with --bwaoption is not able to distinguish illumina 1.8 reads as pair files and throws an error. I use stampy with default (i.e sanger) and -M option. But seems like this is a problem of stam ...
written 7.9 years ago by
lyfsa • 30
0
votes
1
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1.9k
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1
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... stampy: Error: Mixed single- and paired-end in input; BWA can't handle this,
but when I run stampy without --bwaoption, stampy works.
...
written 7.9 years ago by
lyfsa • 30
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