Admin: Pierre Lindenbaum

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Posts by Pierre Lindenbaum

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Comment: C: Understanding the SA tag, Samtools FLAG, and Chimeric Alignments
... > ases, the Samtools Flag will be set to 0, the read is NOT paired (no mate) , mapped, on forward strand, it's a PRIMARY alignment > and the SA tag will also be set. because this reads has also some supplementary alignemnts. Some parts of the read map elswhere, you should find some reads w ...
written 1 day ago by Pierre Lindenbaum116k
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Comment: C: Genomics (DNA) Pipeline - Example
... nextfow pipelines: https://github.com/search?q=bwa+extension%3Anf+HaplotypeCaller (not python) ...
written 3 days ago by Pierre Lindenbaum116k
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Answer: A: How to get number of exons for each transcript in biomart
... ucsc (not biomart) $ mysql --user=genome --host=genome-mysql.soe.ucsc.edu -A -P 3306 -D hg38 -e 'select chrom,name,exonCount from wgEncodeGencodeBasicV28;' +-------+-------------------+-----------+ | chrom | name | exonCount | +-------+-------------------+-----------+ ...
written 3 days ago by Pierre Lindenbaum116k
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Answer: A: Edit header of multifasta file
... try sed '/^>/s/\-.*//' input.fa "for the lines starting with '>', subsitute 'everything after "-"' with empty string" ...
written 4 days ago by Pierre Lindenbaum116k
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Comment: C: samtools " Assertion `iter->curr_off == iter->off[iter->i].v' failed". "
... is your bam sorted ? is your bai file up-to-date ? ...
written 4 days ago by Pierre Lindenbaum116k
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Comment: C: extract fasta sequences using gene names
... look at `grep` with options: `-w` `-A` `-f` ...
written 4 days ago by Pierre Lindenbaum116k
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Comment: C: Detecting Klinefelter from genomic files
... use some BAM files from 1000 genomes as positive controls. You need the BAIs but you don't need the whole BAMs, just the headers. https://twitter.com/brent_p/status/1007759165874302976 ...
written 4 days ago by Pierre Lindenbaum116k
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Answer: A: Detecting Klinefelter from genomic files
... > Klinefelter syndrome (KS) also known as 47,XXY or XXY, is the set of symptoms that result from two or more X chromosomes in males A first idea would be to use the BAI files of your several bams (affected/non-affected) and use [indexcov][1] to quickly get a chart for the sexual chromosomes: ![ ...
written 5 days ago by Pierre Lindenbaum116k
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Comment: C: How to count variant occurrences in .vcf
... for a start: bcftools view input.vcf.gz "chrxxx:12345:12345" |cut -f 10- | tr "\t" "\n" | cut -d ':' -f 1 | sort | uniq -c ...
written 5 days ago by Pierre Lindenbaum116k
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Comment: C: why GATK makes things more complicated ?
... > . Do you have any workflow how to do the analysis? https://github.com/gatk-workflows/ > then tried to align with GATK did not work https://meta.stackexchange.com/questions/147616 ...
written 6 days ago by Pierre Lindenbaum116k

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Popular Question 13 days ago, created a question with more than 1,000 views. For samtools 1.0 'index' : CSI index vs BAI index ?
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