User: salvatore.digiorgio

Reputation:
10
Status:
New User
Location:
ITALIA-FIRENZE-
Last seen:
9 months ago
Joined:
3 years, 7 months ago
Email:
s******************@ittumori.it

Posts by salvatore.digiorgio

<prev • 22 results • page 1 of 3 • next >
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Comment: C: Qualimap problem with Region.bed file
... The issue is comments not introduced by # and dos line ending !!! ...
written 13 months ago by salvatore.digiorgio10
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Comment: C: Qualimap problem with Region.bed file
... Yes, it could be first issue, another could be that column n 4 of bed file has \n at the end of line, my awk command line doesn't remove \n. I will try to adjust these things and i will see. ...
written 13 months ago by salvatore.digiorgio10
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Qualimap problem with Region.bed file
... I am trying to use an Agilent SureSelect exome enrichment bed file in Qualimap. When I run qualimap with the bed file (analyzing a bam), it says that the bed file should have six fields. Here is a sample line from the bed file: chr1 3206095 3207055 gb|AY534250,ens|ENSMUST00000070533,ref|NM_ ...
alignment sequencing written 13 months ago by salvatore.digiorgio10
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Comment: C: Issue with Demultiplex dual indexed Illumina reads using bcl2fastq, for beginner
... This exactly is what I expected ...
written 13 months ago by salvatore.digiorgio10
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Issue with Demultiplex dual indexed Illumina reads using bcl2fastq, for beginners.
... Hi everybody! I am not experienced with sequencing, so maybe there might be a simple solution to the following stuff. We ran a sequencing run on an Illumina NextSeq 500 this week with 100 cycles and dual indices. This is our samplesheet : [Reads] 100 100 [Settings] Adapte ...
index bcl2fastq demultiplexing written 13 months ago by salvatore.digiorgio10
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Comment: C: What's the possible causes of Unbalanced strand mapping in RNA-seq?
... I'm sorry, the TCGA website is messy, and is difficult find the informations. This is what I found: http://embor.embopress.org/content/embor/early/2014/02/17/embr.201337950/DC26/embed/inline-supplementary-material-26.pdf?download=true and on this blog there is just answered question at this link: ...
written 16 months ago by salvatore.digiorgio10
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Comment: C: What's the possible causes of Unbalanced strand mapping in RNA-seq?
... Bam file I used are prepared according to this pipeline https://docs.gdc.cancer.gov/Data/Bioinformatics_Pipelines/Expression_mRNA_Pipeline/ On bam file I used samtools and bcftools. samtools mpileup -Q 15 --max-idepth 8000 -vf GRCh38.d1.vd1.fasta file.bam | bcftools annotate -e "DP<7" | bcf ...
written 16 months ago by salvatore.digiorgio10
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Comment: C: What's the possible causes of Unbalanced strand mapping in RNA-seq?
... The link of my data is https://portal.gdc.cancer.gov/. The information about data i used is at https://cancergenome.nih.gov/abouttcga/aboutdata/platformdesign RNASeqV2 ...
written 16 months ago by salvatore.digiorgio10
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Comment: A: What's the possible causes of Unbalanced strand mapping in RNA-seq?
... Yes, I mean that some position i found show reads aligned only in one strand. I'm using TCGA RNA-seq data, and I read that unstranded library preparation was used, indeed most of my positions show mapping reads either in forward or in revers strand. ![enter image description here][1] [1]: http ...
written 16 months ago by salvatore.digiorgio10
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What's the possible causes of Unbalanced strand mapping in RNA-seq?
... I'm trying to develop pipeline to search for novel RNA editing events. ![enter image description here][1] The last 4 columns are Forward_ref_cov, Forward_alt_cov, Reverse_ref_cov, Reverse_alt_cov Could be artifact? How can i remove these kind of position?? [1]: https://s33.postimg.cc/tbxklr58 ...
strand bias rna-seq written 16 months ago by salvatore.digiorgio10

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