Moderator: i.sudbery

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i.sudbery3.2k
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Sheffield, UK
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IanSudbery
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Posts by i.sudbery

<prev • 290 results • page 1 of 29 • next >
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Comment: C: Filtering sam/bam by using CIGAR deletion sites
... 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.sudbery3.2k
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Comment: C: 1000 genomes coding SNPs not in exonic regions?
... How are you filtering the synonymous and non-synonymous SNPs from all 1000KG SNPs? ...
written 5 hours ago by i.sudbery3.2k
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Comment: C: 1000 genomes coding SNPs not in exonic regions?
... Where are you getting your 1K genome SNPs from? ...
written 5 hours ago by i.sudbery3.2k
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Answer: A: Single cell rna-seq (cel-seq 2) read position shift?
... 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.sudbery3.2k
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Comment: C: How to deduplicate UMI with mapping shift ?
... 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.sudbery3.2k
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Answer: A: is there any statistical way to analysis two groups without replications?
... 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.sudbery3.2k
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Comment: C: is there any statistical way to analysis two groups without replications?
... what sort of data is this? Microarray? TPMs/FPKMs from an RNA-seq experiment? ...
written 9 hours ago by i.sudbery3.2k
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Comment: C: is there any statistical way to analysis two groups without replications?
... 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.sudbery3.2k
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Comment: C: Upgrade to 3.18 no longer allows optional parameters to be omitted
... Can you please clarify which tool it is you have upgraded from 3.15 to 3.18? ...
written 1 day ago by i.sudbery3.2k
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Comment: C: Classification using publicly available RNA-seq dataset
... These generally only exist for things in GEO or public SRA of course. ...
written 1 day ago by i.sudbery3.2k

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Scholar 8 hours ago, created an answer that has been accepted. For A: How to only change/substitute every QNAME(Read ID) from a Bam file?
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Teacher 5 days ago, created an answer with at least 3 up-votes. For A: Filtering during RNA Seq analysis?
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Scholar 6 days ago, created an answer that has been accepted. For A: How to only change/substitute every QNAME(Read ID) from a Bam file?
Scholar 8 days ago, created an answer that has been accepted. For A: How to only change/substitute every QNAME(Read ID) from a Bam file?
Teacher 9 days ago, created an answer with at least 3 up-votes. For A: Filtering during RNA Seq analysis?
Scholar 11 days ago, created an answer that has been accepted. For A: How to only change/substitute every QNAME(Read ID) from a Bam file?
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Commentator 19 days ago, created a comment with at least 3 up-votes. For C: if I am right about miRNA DE workflow
Scholar 19 days ago, created an answer that has been accepted. For A: How to only change/substitute every QNAME(Read ID) from a Bam file?
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Scholar 8 weeks ago, created an answer that has been accepted. For A: How to only change/substitute every QNAME(Read ID) from a Bam file?
Scholar 10 weeks ago, created an answer that has been accepted. For A: How to only change/substitute every QNAME(Read ID) from a Bam file?
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Commentator 10 weeks ago, created a comment with at least 3 up-votes. For C: if I am right about miRNA DE workflow
Popular Question 3 months ago, created a question with more than 1,000 views. For List of replication dependent and independent histone genes
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