User: a.james

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a.james110
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Germany
Last seen:
5 months ago
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4 years ago
Email:
a******@dkfz-heidelberg.de

Posts by a.james

<prev • 52 results • page 1 of 6 • next >
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Comment: C: Error while parsing vcf file
... @Pierre Lindenbaum, apparently the issue is with vcf.reader parser doesn't suit for vcf 4.2 files. ...
written 15 months ago by a.james110
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Comment: C: Error while parsing vcf file
... No, I just highlighted it for bio-stars. There is no quote in real vcf file. ...
written 15 months ago by a.james110
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Comment: C: Error while parsing vcf file
... Here is the whole line which complaints, #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT TUMOR NORMAL 1 14748 . G C . alt_allele_in_normal;t_lod_fstar ECNT=1;HCNT=4;MAX_ED=.;MIN_ED=.;NLOD=29.34;TLOD=4.58;CSQ=C|non_coding_transcript_exon_variant|MODIFIER|WASH7P ...
written 15 months ago by a.james110
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Comment: C: Error while parsing vcf file
... Thats the first line of my vcf file I mean after header, and I am wondering 82, 2 is in int format isnt? ...
written 15 months ago by a.james110
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Error while parsing vcf file
... Hello, I am trying to convert my multiple vcf file into a tabular format. And I am having error while parsing through each row of the file here is part of the script, for files in results: Va_BM = vcf.Reader(filename=files, compressed=False) for variant in Va_BM: ...
vcf rna-seq snp sequencing written 15 months ago by a.james110
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How to get the number of exon within genes from GRCH37 reference
... Dear All, How would get a list with number exons for all non-coding genes? Any suggestion would be really great Thank you ...
gene next-gen rna-seq written 16 months ago by a.james110 • updated 16 months ago by Pierre Lindenbaum111k
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Comment: C: Querying positions (bed file) towards BAM files using samtools mpileup
... The prefix for both the query bed file and genome file for chromosomes has no "chr". And so I don't think that the potential reason ...
written 18 months ago by a.james110
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Comment: C: Querying positions (bed file) towards BAM files using samtools mpileup
... I didn't get any error message. Whereas I got an empty vcf file (I mean there is header but no results). I am supposed to get a vcf file with read depth and all the information I asked in the parameter of command line. ...
written 18 months ago by a.james110
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Querying positions (bed file) towards BAM files using samtools mpileup
... Dear All, I need to query a set of chromosomal positions towards a couple of BAM files, and I am using samtools mpileup for this. Following is my command line, samtools mpileup -L 1000000 -u -A -B -d 100000 -Q 0 -t DP -t AD -t ADF -t ADR -f GRCh37.fa --positions mybed.bed sample1.bam sample2 ...
rna-seq written 18 months ago by a.james110
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Comment: C: GeneSCF gives out more pathways for genes compared to DAVID
... 1. Thank you so much its very clear .. 2: Which version of GeneSCF are you using ? It looks like you are using V1.0 !!! , Yes you are right. I have tried the both versions..And with the old version v1.0 has considerable overlap with pathways from other platform for comaprision study. This is the ...
written 2.1 years ago by a.james110

Latest awards to a.james

Great Question 5 months ago, created a question with more than 5,000 views. For ALL RNA-seq publicly available data
Popular Question 8 months ago, created a question with more than 1,000 views. For BED file with amplicon information
Great Question 13 months ago, created a question with more than 5,000 views. For ALL RNA-seq publicly available data
Popular Question 14 months ago, created a question with more than 1,000 views. For How to find the frame shift information from fusion gene sequence
Popular Question 14 months ago, created a question with more than 1,000 views. For DESeq output from RNA-seq
Popular Question 20 months ago, created a question with more than 1,000 views. For ALL RNA-seq publicly available data
Student 24 months ago, asked a question with at least 3 up-votes. For ALL RNA-seq publicly available data
Popular Question 24 months ago, created a question with more than 1,000 views. For ALL RNA-seq publicly available data
Popular Question 2.1 years ago, created a question with more than 1,000 views. For ALL RNA-seq publicly available data
Scholar 2.1 years ago, created an answer that has been accepted. For A: GeneSCF gives out more pathways for genes compared to DAVID
Supporter 2.1 years ago, voted at least 25 times.
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Pathway Graphs for gene set from RNA-seq
Popular Question 2.6 years ago, created a question with more than 1,000 views. For ALL RNA-seq publicly available data
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