User: shumaila.sayyab
shumaila.sayyab • 0
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Posts by shumaila.sayyab
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Comment:
C: sciClone input LOH
... perhaps, this may be the answer to what i was looking.. which i missed earlier
https://www.biostars.org/p/251007/ ...
written 13 months ago by
shumaila.sayyab • 0
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... Dear all,
I want to use sciclone on my somatic variant data. I am confused about the input it takes. One is the CNA information but incase of LOH input file, Is it cnLOH or LOH ? what i mean is looking at the results from ASCAT, should i give regions where we have major 2n and monir 0, or all the ...
written 13 months ago by
shumaila.sayyab • 0
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Comment:
C: Breakdancer output error
... Thankyou ernfrid, it worked after giving unique library names.
...
written 3.8 years ago by
shumaila.sayyab • 0
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C: Breakdancer output error
... Thanks ernfrid, did this answer your question? please let me know if you have nay suggestion for the conf. file??
...
written 3.8 years ago by
shumaila.sayyab • 0
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C: Breakdancer output error
... I think Yes, each of my sample has two libraries (tight and wide), and when i run the script to generate the configuration file, i received this file (attached)
readgroup:sample1_tight platform:Illumina map:../sample1_sample.dedup.bam readlen:50.80 lib:tight num:10001 lower:2298.0 ...
written 3.8 years ago by
shumaila.sayyab • 0
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...
Hi everyone,
I have 4 samples (matepair illumina) and run Breakdancer_max as follows:
bam2cfg.pl -h -g -q 10 sample1.bam sample2.bam sample3.bam sample4.bam >sample1_2_sample3_4.cfg
it worked without error msg.
breakdancer-max -o chrX -q 10 -d Fastq_SVReadsFile_X -g GBrow ...
written 3.8 years ago by
shumaila.sayyab • 0
• updated
3.8 years ago by
ernfrid • 190
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