User: pbigbig

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pbigbig180
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Posts by pbigbig

<prev • 86 results • page 1 of 9 • next >
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extract SNPs corresponding position on BLAST subject sequence
... Hi everyone, I have run BLAST a transcript containing SNP against genome and get result like this (outfmt6) TRINITY_DN25200_c0_g1_i2@4719A--T scaffold75_cov195 99.031 3303 15 4 1506 4807 13900341 13903627 0 5906 Since the position of SNP is 4719 on the transcript, could you tell me how to tra ...
snp blast extract sequence written 7 weeks ago by pbigbig180
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Comment: C: Adding Domain Annotation Identifiers To Fasta Headers
... Hi, Thank you very much. could you please add some modification so that this could work on multiple-line fasta. If possible, some detail explanation regarding those commands would be great. Thanks ...
written 8 weeks ago by pbigbig180
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Comment: C: Merging BAM file before running GATK or merging vcf output
... thank you for your opinion! ...
written 3 months ago by pbigbig180
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Merging BAM file before running GATK or merging vcf output
... Hi everyone, I have 2 data sets (in FASTQ) of 2 samples with contrast phenotype. I could possibly perform these workflows: 1. Map 2 data sets to a reference transcriptome (not genome), processing individual BAM files, run GATK HaplotypeCaller, got 2 vcf files output, merge 2 vcf files into final o ...
vcf gatk snp written 3 months ago by pbigbig180 • updated 3 months ago by Lila M 370
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Answer: A: How to run Interproscan on cluster ?
... Hi, I suggest that you download the binary files of sfld from here: ftp://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/bin/ then replace all files in ${INTERPROSCAN5HOME}/bin/sfld/ with them, it worked for me. ...
written 7 months ago by pbigbig180
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Comment: C: Transcriptomes comparison and check for shared transcripts with arbitrary simila
... Thanks for your suggestion, I will BLAT them to each other. Sorry for my clumsy explanation, for short, I just have RNAseq data from different individuals (same tissue and species), some of them are pretty small sized compared to others after deduplicate (because of PCR artifacts), therefore I would ...
written 7 months ago by pbigbig180
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Transcriptomes comparison and check for shared transcripts with arbitrary similarity
... Hi everyone, I have Illumina RNAseq data from individuals of 2 groups (2 different phenotypes), after preprocessing reads and running de novo assembly with Trinity, I have group 1st with assemblies sized from 45-55 Mb (megabyte, fasta format) and another group (group 2nd) with assemblies sized from ...
rnaseq de novo assembly transcriptome written 9 months ago by pbigbig180
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Comment: C: Confusion regarding Trinity analyze_diff_expr.pl
... thank you for your suggestion ! ...
written 10 months ago by pbigbig180
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(Closed) Confusion regarding Trinity analyze_diff_expr.pl
... Hi all, I have some confusion regarding 2 ways of usage of `analyze_diff_expr.pl` script in Trinity package. 1. In the usage instruction resides within script, we have to input matrix file: `${name}.TMM.EXPR.matrix` , as in: > # Required: > # > # --matrix TMM.EXPR. ...
trinity differential expression transcriptome written 11 months ago by pbigbig180
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Confusion regarding Trinity analyze_diff_expr.pl
... Hi everyone, I have some confusion regarding two ways of usage of `analyze_diff_expr.pl` script in the Trinity package. In the usage instruction resides within script, we have to input matrix file: `${name}.TMM.EXPR.matrix` , as following: > # Required: > # > # --matrix ...
trinity differential expression transcriptome written 11 months ago by pbigbig180 • updated 10 months ago by Farbod3.0k

Latest awards to pbigbig

Popular Question 8 weeks ago, created a question with more than 1,000 views. For Extracting ids of a cluster in heatmap
Popular Question 8 weeks ago, created a question with more than 1,000 views. For Extracting ids of a cluster in heatmap
Popular Question 4 months ago, created a question with more than 1,000 views. For Scaffolding with SSPACE returned scaffold the same as initial contigs set
Popular Question 7 months ago, created a question with more than 1,000 views. For Jellyfish -C option explanation
Great Question 9 months ago, created a question with more than 5,000 views. For Run multiple fastq.gz files with FastQC and yield single report?
Popular Question 10 months ago, created a question with more than 1,000 views. For Jellyfish -C option explanation
Popular Question 10 months ago, created a question with more than 1,000 views. For kmergenie can not execute on a file because directory not exist?
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Popular Question 22 months ago, created a question with more than 1,000 views. For Run multiple fastq.gz files with FastQC and yield single report?

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