User: Bioinfonext

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Bioinfonext190
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Posts by Bioinfonext

<prev • 374 results • page 1 of 38 • next >
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Comment: C: cat command to get multiple fq reads into single fastq file
... thanks you very much! ...
written 28 days ago by Bioinfonext190
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cat command to get multiple fq reads into single fastq file
... Hi, file names are like this: Root_T1_S_R8_S48_unmapped.R1.fq Root_T1_S_R9_S47_unmapped.R1.fq Root_T2_F_R2_S25_unmapped.R2.fq Root_T2_F_R3_S24_unmapped.R2.fq I need to take Multiple R1.fq and R2.fq into two separate files to run trinity for de novo assembly. I am little bit ...
rna-seq linux written 28 days ago by Bioinfonext190
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Comment: C: extract unmapped pair end read from sam files
... Hi Genomax, thanks for your all help. above command seems very confusing for me as it only generate a single fastq files if I run it on sam file as well. instead of this I am using the below three command in loop command one by one as suggest by you earlier: if I come across any issue, will let yo ...
written 6 weeks ago by Bioinfonext190
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extract unmapped pair end read from sam files
... Hi, I do have multiple pair end sam files. I am thinking to use below command to extract unmapped read from all sam files to bam files by using below command and after this I am trying to use reformat.sh from bbtools to extract the unmapped read pair from bam file. Is there any way to run the ref ...
samtools bbtools rna-seq linux written 6 weeks ago by Bioinfonext190 • updated 6 weeks ago by genomax76k
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RNAseq read mapping statistics from sam file
... Hi, I used below script to run Hisat2 for multiple pair end read files to map on reference genome separately. I got the sam file but it did not generate the statistics of read mapping, is it still possible to get read mapping statistics from sam files? #!/bin/bash #SBATCH --job-name=mpi_jo ...
hisat2 rna-seq bash written 7 weeks ago by Bioinfonext190
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Comment: C: How to generate a combined read count txt file with header as file name
... thanks Lieven, your script works perfectly. Thanks Again bioinfonext ...
written 4 months ago by Bioinfonext190
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Comment: C: How to generate a combined read count txt file with header as file name
... Hi Pierre, I am having 60 read count txt file so should I keep adding all like you have shown with two files. Thanks Bioinfonext ...
written 4 months ago by Bioinfonext190
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Comment: C: How to generate a combined read count txt file with header as file name
... Hi genomax, I used HTSeq for read count and I am having like 60 read count txt files. Thanks Bioinfonext ...
written 4 months ago by Bioinfonext190
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How to generate a combined read count txt file with header as file name
... I do have multiple txt file for RNAseq read count, is it possible to generate a single txt file with the file name as column header; txt file having read count like this: so first column is same in all files. BGIOSGA000001 0 BGIOSGA000002 12 BGIOSGA000003 0 BGIOSGA000004 0 ...
R bash awk linux written 4 months ago by Bioinfonext190
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Comment: C: HOW TO remove all spaces except first space with semicolon
... thanks for your all help. this command works for me: cat final.taxonomy.txt | tr "\r" "\n" > final.taxonomy2.txt Thanks again Bioinfonext ...
written 4 months ago by Bioinfonext190

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