Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • abedkurdi
    replied
    You can do the following:
    for f in /Users/xxx/Desktop/Index_align/Fastq/fastq_run4/*.fastq.gz; do
    name=$(basename $f _L001_R1_001.fastq.gz)
    bwa sampe /Users/xxx/Desktop/Index_align/GRCh37_latest_genomic.fna \
    ${name}_L001_read1.sai ${name}_L001_read2.sai \
    ${name}_L001_R1_001.fastq.gz ${name}_L001_R2_001.fastq.gz > ${name}_aln.sam
    done

    Leave a comment:


  • Kax
    started a topic Loop in bwa commands

    Loop in bwa commands

    Hiya,

    I'm trying to loop multiple input files with matching prefixes and different file types in bwa sampe ; here's the general structure:
    Code:
    bwa sampe /Users/xxx/Desktop/Index_align/GRCh37_latest_genomic.fna H2_S16_L001_read1.sai H2_S16_L001_read2.sai \
    H2_S16_L001_R1_001.fastq.gz H2_S16_L001_R2_001.fastq.gz > aln_H2_S16_L001.sam
    I'm trying to make a loop like:
    Code:
    for i in /Users/xxx/Desktop/Index_align/Fastq/fastq_run4/ \
    do bwa sampe /Users/xxx/Desktop/Index_align/GRCh37_latest_genomic.fna \
    $i\-read1.sai $i\-read2.sai $i\-R1_001.fastq.gz $i\-R2_001.fastq.gz > $i\-aln.sam; done
    Does anyone have suggestions for what I am missing? Like perhaps I need to create a list of the prefix file names? I would greatly appreciate any advice. Thanks!

Latest Articles

Collapse

  • seqadmin
    Multiomics Techniques Advancing Disease Research
    by seqadmin


    New and advanced multiomics tools and technologies have opened new avenues of research and markedly enhanced various disciplines such as disease research and precision medicine1. The practice of merging diverse data from various ‘omes increasingly provides a more holistic understanding of biological systems. As Maddison Masaeli, Co-Founder and CEO at Deepcell, aptly noted, “You can't explain biology in its complex form with one modality.”

    A major leap in the field has
    ...
    02-08-2024, 06:33 AM
  • seqadmin
    The 3D Genome: New Technologies and Emerging Insights
    by seqadmin


    The study of three-dimensional (3D) genomics explores the spatial structure of genomes and their role in processes like gene expression and DNA replication. By employing innovative technologies, researchers can study these arrangements to discover their role in various biological processes. Scientists continue to find new ways in which the organization of DNA is involved in processes like development1 and disease2.

    Basic Organization and Structure
    Understanding...
    01-22-2024, 03:25 PM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, Today, 08:57 AM
0 responses
9 views
0 likes
Last Post seqadmin  
Started by seqadmin, 02-14-2024, 09:19 AM
0 responses
42 views
0 likes
Last Post seqadmin  
Started by seqadmin, 02-12-2024, 03:37 PM
0 responses
402 views
0 likes
Last Post seqadmin  
Started by seqadmin, 02-09-2024, 03:36 PM
0 responses
646 views
0 likes
Last Post seqadmin  
Working...
X