User: sheetalshetty13

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Posts by sheetalshetty13

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Comment: C: Sample Sam File
... Version is important. I just found out -s option is not available on version 0.1.16 Also option is cryptic: so I had to write it as -s -1.5 ( to get 50% of reads) -s -1.7 ( to get 70% of reads) 1 is the seed and .5/.7 the percent of reads for sub sampling ...
written 3.9 years ago by sheetalshetty1340
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Comment: C: Sample Sam File
... I could not find the -s option on samtools. When I tried using, gave me an error 'invalid option'. Would you know the reason. I am using samtools-0.1.16 ...
written 3.9 years ago by sheetalshetty1340
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Comment: C: Breakdancer
... Many thanks!!! I have only translocation reads in my file. I did not include any normal reads. I used wgsim to create fastqs and did alignment using bwa with default parameters to get bam files. However, the insert size distribution with my data shows a normal curve. I will definitely create anothe ...
written 3.9 years ago by sheetalshetty1340
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Breakdancer
... I have a config file out of Breakdancer that looks like below: readgroup:transl_RG platform:illumina map:transl_RG.sorted.bam readlen:70.00 lib:transl_RG num:10001 lower:8.44 upper:996.38 mean:499.94 std:49.40 SWnormality:-2.61 flag:18(99.97%)32(0. ...
breakdancer written 3.9 years ago by sheetalshetty1340 • updated 3.9 years ago by Charles Warden4.9k
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Binning Of Chromosome Data
... Hi I would like to bin my chromosome data in 1 Mbps bins. The data looks as below: Chromosome Start End chr1 15892 16421 chr1 17801 17812 chr2 24136 24223 I would like the output to look something like this: Chr Start End Count chr1 1 1000000 4 chr1 1000000 2000000 10 ...
awk written 4.6 years ago by sheetalshetty1340 • updated 4.6 years ago by Ido Tamir4.8k

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