User: swarajgaikwad15

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Posts by swarajgaikwad15

<prev • 29 results • page 1 of 3 • next >
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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 29 days ago by swarajgaikwad150
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Comment: C: MarkDuplicates: Mates are missing
... @ATpoint, any guess to solve this issue. ...
written 4 weeks 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 5 weeks ago by swarajgaikwad150 • updated 5 weeks ago by ATpoint17k
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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 12 weeks ago by swarajgaikwad150 • updated 12 weeks ago by Devon Ryan90k
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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 4 months ago by swarajgaikwad150 • updated 4 months ago by ATpoint17k
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Comment: C: What can be done to separate the healthy and patient samples in PCA plot and Dis
... Thank you for your reply, Kevin, I have read DESeq2 vignette but it didn't find anything about solving such kind of error, however, Again i'll read and find it out what can be done. But as per your experience, can you give me any suggestions for solving this problem? Thank you ...
written 5 months ago by swarajgaikwad150
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Comment: C: What can be done to separate the healthy and patient samples in PCA plot and Dis
... Actually, I have transformed my raw counts using rlog and then I am visualizing my data in PCA plot and heatmap so that I could obtain proper Differential expressing genes. ...
written 5 months ago by swarajgaikwad150
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What can be done to separate the healthy and patient samples in PCA plot and Distance matrix
... Hello, I am doing RNA seq analysis to obtain Differential expression genes using DESeq2 for 13 patient and 6 Healthy donors. Before going for DESeq2 analysis, I am visualizing my samples by Distance matrix and PCA plot, using the following commands: library("RColorBrewer") sampleDistMatrix ...
pca plot distance matrix deseq2 rna-seq written 5 months ago by swarajgaikwad150

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