User: marongiu.luigi

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Posts by marongiu.luigi

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Comment: C: Can two mates have different file size?
... Ops, I forgot. you are right with zcat it becomes: $ zcat 501N-1_1.fq.gz | wc -l 933442092 $ zcat 501N-1_2.fq.gz | wc -l 933442092 So the file size is not useful. Thanks. ...
written 13 hours ago by marongiu.luigi230
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Comment: C: Can two mates have different file size?
... In that case, still there are differences: $ wc -l 501N-1_1.fq.gz 63553348 501N-1_1.fq.gz $ wc -l 501N-1_2.fq.gz 62303198 501N-1_2.fq.gz The numbers should be divided by 4 to give the number of reads, but it is clear that are different. Thanks anyway to all. ...
written 1 day ago by marongiu.luigi230
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Can two mates have different file size?
... Hello I wanted to ask if it is possible for two paired files -- from paired end sequencing -- to have a different byte size, for instance: -rw------- 1 m G300 18759221836 Jun 11 11:26 501N-1_1.fq.gz -rw------- 1 m G300 19584616095 Jun 11 11:36 501N-1_2.fq.gz Probably this is fine beca ...
fastq sequencing written 1 day ago by marongiu.luigi230
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Comment: C: Solve SAM issues flagged by Picard's ValidateSamFile
... from this [post][1], I found that to recreate the fastq files I need the non sorted BAMs, thus I now keep the unsorted 'just in case' I need to re-generate fastq for subsets of the alignment [1]: https://www.biostars.org/p/326714/#327275 ...
written 2 days ago by marongiu.luigi230
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Comment: C: Solve SAM issues flagged by Picard's ValidateSamFile
... OK, I'll skip trimming. For order you mean lane 1 after lane 2 etc? ...
written 2 days ago by marongiu.luigi230
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Comment: C: Solve SAM issues flagged by Picard's ValidateSamFile
... yes, I know but I prefer to keep the original unsorted BAM just in case... ...
written 2 days ago by marongiu.luigi230
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Solve SAM issues flagged by Picard's ValidateSamFile
... Dear all, I aligned fastq pairs to the human genome with BWA MEM, including the read group flag. The fastq files were trimmed for quality with trimmomatic.sh PE -phred33 -threads 8 \ \ \ LEADING:13 TRAILING:13 SLIDINGWINDOW:7:30 MINLEN:30 Since each sample had multiple fil ...
sam file alignment error picard written 2 days ago by marongiu.luigi230
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Comment: C: Identify insertions with IGV
... OK then, IGV is not the tool for checking insertion sites. I will use other tools. If there are other suggestions over lumpy I will be happy to check them. Thank you. ...
written 7 days ago by marongiu.luigi230
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Comment: C: Identify insertions with IGV
... yes. since there are 3 types of mutations in msbar (insertion, deletion, substitutions), there should be in theory 500/3 insertions points. ...
written 8 days ago by marongiu.luigi230
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Comment: C: Identify insertions with IGV
... The figure I get after colouring for the INSERT SIZE (and INSERT SIZE AND PAIR ORIENTATION) is this: ![enter image description here][1] With a bit of imagination, one could argue that there is a purple blob in the centre of the genome, where should be the insertion point. This is the enlargement: ...
written 8 days ago by marongiu.luigi230

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