Moderator: i.sudbery
i.sudbery ♦ 3.2k
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- IanSudbery
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Posts by i.sudbery
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... import pysam
inbam = pysam.AlignmentFile("my_bamfile.bam")
outbam = pysam.AlignmentFile("filtered_bamfile.bam", template=inbam)
for read in inbam.fetch(until_eof=True):
if read.mapping_quality > 30 and 'D' in read.cigarstring:
outbam.write(read)
...
written 3 hours ago by
i.sudbery ♦ 3.2k
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61
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0
answers
... How are you filtering the synonymous and non-synonymous SNPs from all 1000KG SNPs? ...
written 5 hours ago by
i.sudbery ♦ 3.2k
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0
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61
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0
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... Where are you getting your 1K genome SNPs from? ...
written 5 hours ago by
i.sudbery ♦ 3.2k
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1
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679
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1
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... Sorry for the delay, but I thought I should add this for the record.
CEL-Seq2 adds the UMI in the RT stage of the sample prep, but fragmentation happens later. Thus multiple copies of the same original fragment can have different mapping co-ordinates. This is a common property of most 3' tagging pr ...
written 8 hours ago by
i.sudbery ♦ 3.2k
0
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123
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... You should check whether, where you see cases of reads mapping to adjacent bases with the same UMI, the reads mapping to one location are soft-clipped - that is the actual start of the read is at the same base, even if the mapping co-ordinate given in the BAM file is different. ...
written 8 hours ago by
i.sudbery ♦ 3.2k
2
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2
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69
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2
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... Without replicates it is pretty much meaningless to do differential analysis as it is impossible to find the variability for each gene. In a child-vs-parent comparison there is *some* ability to measure variance, because you have both mother and father, and conceptually you can measure the mother-fa ...
written 8 hours ago by
i.sudbery ♦ 3.2k
0
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2
answers
69
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2
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... what sort of data is this? Microarray? TPMs/FPKMs from an RNA-seq experiment? ...
written 9 hours ago by
i.sudbery ♦ 3.2k
0
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2
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69
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2
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... Do you want to do this on a gene-by-gene basis - i.e. you'd like to know which genes are different in the child than in the parents?
Or just if the child, in general, in different from the parents "averaging" across all genes?
Also do you want to do child vs. "parents", or child vs mother and child ...
written 10 hours ago by
i.sudbery ♦ 3.2k
0
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1
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105
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1
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... Can you please clarify which tool it is you have upgraded from 3.15 to 3.18? ...
written 1 day ago by
i.sudbery ♦ 3.2k
0
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1
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142
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1
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... These generally only exist for things in GEO or public SRA of course. ...
written 1 day ago by
i.sudbery ♦ 3.2k
Latest awards to i.sudbery
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For A: How to only change/substitute every QNAME(Read ID) from a Bam file?
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For A: Alternative to Cufflinks ?
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For A: Filtering during RNA Seq analysis?
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For A: Filtering during RNA Seq analysis?
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For A: Filtering during RNA Seq analysis?
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For A: How to only change/substitute every QNAME(Read ID) from a Bam file?
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8 days ago,
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For A: Filtering during RNA Seq analysis?
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11 days ago,
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For A: How to only change/substitute every QNAME(Read ID) from a Bam file?
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11 days ago,
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For A: Filtering during RNA Seq analysis?
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19 days ago,
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For C: if I am right about miRNA DE workflow
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19 days ago,
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For A: How to only change/substitute every QNAME(Read ID) from a Bam file?
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19 days ago,
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For A: Filtering during RNA Seq analysis?
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8 weeks ago,
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For A: Filtering during RNA Seq analysis?
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For A: Alternative to Cufflinks ?
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For A: How to only change/substitute every QNAME(Read ID) from a Bam file?
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10 weeks ago,
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For A: How to only change/substitute every QNAME(Read ID) from a Bam file?
Teacher
10 weeks ago,
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For A: Filtering during RNA Seq analysis?
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For A: How to only change/substitute every QNAME(Read ID) from a Bam file?
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