User: pbigbig

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pbigbig190
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Posts by pbigbig

<prev • 89 results • page 1 of 9 • next >
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Mapping both PE reads and Single-end reads into transcriptome
... Hi everybody, I built several de novo transcriptomes from non-model organism without genome reference by Trinity. Sequencing libraries were prepared with stranded method (dUTP), therefore I only used paired-end reads with RF SS_lib_type parameter in Trinity for assembling. However, earlier preproce ...
trinity strand-specific differential expression written 20 minutes ago by pbigbig190
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Comment: C: Masking short sequences between gaps in genome assembly
... Hi, I mean to hard masking it, which would turn any A C G T to N ...
written 9 weeks ago by pbigbig190
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Masking short sequences between gaps in genome assembly
... Hi, I have assembled a genome, using Illumina Pair-end reads for assembling, Mate pair reads for scaffolding. In resulted fasta files, I notice some patterns like this: ...NNNNNNNNNNNNNNNNGTGTGTAGGATCTCACNNNNNNNNNNNNNNNNNNNNNN... I would like to hardmask those small "island" sequences between gap ...
masking genome assembly written 9 weeks ago by pbigbig190
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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 12 months ago by pbigbig190 • updated 10 months ago by Biostar ♦♦ 20
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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 13 months ago by pbigbig190
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Comment: C: Merging BAM file before running GATK or merging vcf output
... thank you for your opinion! ...
written 14 months ago by pbigbig190
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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 14 months ago by pbigbig190 • updated 14 months ago by Lila M 390
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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 18 months ago by pbigbig190
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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 19 months ago by pbigbig190
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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 20 months ago by pbigbig190

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Popular Question 2 days ago, created a question with more than 1,000 views. For Merging assemblies with GAM-NGS
Popular Question 27 days ago, created a question with more than 1,000 views. For Merging assemblies with GAM-NGS
Epic Question 4 months ago, created a question with more than 10,000 views. For Run multiple fastq.gz files with FastQC and yield single report?
Popular Question 6 months ago, created a question with more than 1,000 views. For Merging assemblies with GAM-NGS
Popular Question 6 months ago, created a question with more than 1,000 views. For Merging assemblies with GAM-NGS
Popular Question 6 months ago, created a question with more than 1,000 views. For Merging assemblies with GAM-NGS
Popular Question 13 months ago, created a question with more than 1,000 views. For Extracting ids of a cluster in heatmap
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Popular Question 15 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 18 months ago, created a question with more than 1,000 views. For Jellyfish -C option explanation
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