User: swarajgaikwad15

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Posts by swarajgaikwad15

<prev • 32 results • page 1 of 4 • next >
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Comment: C: Volcano plot: Using Multiple results
... Yes this can be a good method, Thank you @shawn.w.foley ...
written 3 months ago by swarajgaikwad150
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Comment: C: Volcano plot: Using Multiple results
... Thanks a lot @ATpoint. It worked. and Since I am working on very small no. of genes, plot is not that messy. I appreciate your suggestions. ...
written 3 months ago by swarajgaikwad150
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Volcano plot: Using Multiple results
... Hello, I am trying to make volcano plot of the multiple microarray results data in the single plot itself and annotating them by different colors. I know how to generate the Volcano plot for single result, but the same logic I can't apply for multiple results. I googled it but there also i didn't ge ...
volcanoplot microarray rna-seq written 3 months ago by swarajgaikwad150 • updated 3 months ago by shawn.w.foley1.1k
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Comment: C: MarkDuplicates: Mates are missing
... Two fastq files are paired (-1/-2), and the remaining two are unpaired (-U) This is one of my [post][1] [1]: https://www.biostars.org/p/360675/ ...
written 5 months ago by swarajgaikwad150
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Comment: C: MarkDuplicates: Mates are missing
... @ATpoint, any guess to solve this issue. ...
written 5 months ago by swarajgaikwad150
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Comment: C: MarkDuplicates: Mates are missing
... java -jar trimmomatic-0.38.jar PE -threads 4 -phred33 S1_1.fastq.gz S1_2.fastq.gz S1_1p.fastq.gz S1_1u.fastq.gz S1_2p.fastq.gz S1_2u.fastq.gz ILLUMINACLIP:TruSeq3-PE.fa:2:30:10:1:true LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36 ...
written 6 months ago by swarajgaikwad150 • updated 6 months ago by ATpoint25k
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MarkDuplicates: Mates are missing
... Hello, I am stuck in the problem of 'ValidateSamFile' of picard tools. I have checked this problem on different forums, but I didn't find any solution there. I have used Hisat2 for the alignment of the paired-end fastq files (obtained after trimming by using trimmomatic tool) against Ensembl refere ...
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free(): invalid next size (normal) Aborted (core dumped)
... I am using gffread software, for obtaining fasta sequence from gtf file, gffread -w transcripts.fa -g /path/to/reference_genome/genome.fa 'input/transcript.gtf but I am facing an error > 'free(): invalid next size (normal)' > 'Aborted (core dumped)' Although the output file ' ...
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Warning: gene "NR_111945" (on chr1) has reference transcripts on both strands?
... Hello, I am using Stringtie tool for quantification purpose, in order to skip 'MSTRG.xx' , this time I have used -e option in the following command stringtie '/path/to/input_file/inputfile.bam' -G '/path/to/ref/hg38ucsc.gtf' -o output.gtf -p 8 -e -A output_abundance.out Here I am facing the f ...
stringtie rna-seq written 7 months ago by swarajgaikwad150 • updated 7 months ago by Devon Ryan92k
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Hisat2 after the use of trimmomatic software: (ERR): hisat2-align exited with value 134
... I have used trimmomatic software for trimming my paired-end RNA-Seq data, Now I have four output results viz.: sample_1p.fq.gz, sample_1u.fq.gz, sample_2p.fq.gz, and sample_2u.fq.gz. I followed this [Question][1] Which suggests using both samples paired and unpaired separately for alignment and th ...
trimmomatic new tuxedo protocol rna-seq hisat2 written 9 months ago by swarajgaikwad150 • updated 9 months ago by ATpoint25k

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