Readfilescommand gunzip -c
WebFeb 15, 2024 · I believe it is because my --readFilesCommand gunzip -c command was only unzipping the first file and not the second and therefore the second .fq.gz file was unreadable. I have now unzipped both files and run the command without --readFilesCommand and it has worked. However, I don't want to have to do this for all of … WebSep 17, 2024 · RNA-seq 比对软件STAR——（2）使用 一、参数说明 详见——>manual （1） readFilesIn 要映射序列文件的名称（带路径），注如果文件是压缩的文件使用readFilesCommand参数进行解压缩。如果是（*.gz）使用 --readFilesCommand zcat或 --readFilesCommand gunzip -c，对于bzip2压缩文件，使用–readFilesCommand bunzip2 -c …
Readfilescommand gunzip -c
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Web–readFilesCommand gunzip -c : use “gunzip -c” to uncompress FASTQ on-the-fly, since it is gzipped –outFileNamePrefix : prefix (and path) to use for all output files –quantMode … WebMar 24, 2024 · Actually, you can use the bash shell hack < (gunzip -c filename.gz) to pass the gzipped file (or similarly, any other kind of zip file), which doesn't have a built-in mechanism to read the zipped files directly (STAR is awesome in providing the built-in mechanism :). It uses a trick of shell called Process Substitution.
WebMay 26, 2024 · Then, I tried to aligned the reads like this: STAR --genomeDir output/index --readFilesIn reads.fastq.gz --readFilesCommand gunzip -c --outFileNamePrefix output/alignment --quantMode GeneCounts --outSAMunmapped None --outSAMtype BAM SortedByCoordinate --outSAMattrRGline ID:RG1 CN:yy \"DS: z z z\" SM:sample WebOct 12, 2024 · cat ids parallel echo STAR --runThreadN 12 --genomeDir $IDX --readFilesCommand gunzip -c --readFilesIn $INP/ {}_1_trimmed.fq.gz\ --sjdbGTFfile $GTF --outFileNamePrefix $RES --limitGenomeGenerateRAM 32000000000 \ --outSAMtype BAM SortedByCoordinate > run.sh
WebI tried using zcat and gunzip in STAR to unzip the input files. The program runs fine but the output (aligned bam file is 0kb) has nothing in it. There was no mapping done (mapping is 0%), the same code runs fine if I use the fastq file instead of fastq.gz Has anyone experienced the same? Code is: WebThe way to say that in Python is simply 'gunzip -c'. – tripleee Sep 30, 2024 at 12:08 Thank you tripleee! Very informative answer, I'm new to using bash so that's why I used the …
Webgunzip -k gencode.v29.annotation_chr10.gtf.gz gunzip -k Homo_sapiens.GRCh38.dna.chromosome.10.fa.gz This works on any Linux: ... (–readFilesCommand) The following options are optional: type of output (–outSAMtype). Defaul is “BAM Unsorted”; STAR outputs unsorted Aligned.out.bam file(s). “The paired …
WebOct 16, 2024 · P1_2.fq.gz \ --readFilesCommand zcat \ --outSAMtype BAM SortedByCoordinate \ --outFileNamePrefix /Users bulkRNA/3.bam/P132 P132 and I got the … csp eastern healthWebNov 27, 2024 · If the read files are gzip compressed (*.fastq.gz), you can add an additional --readFilesCommand zcat or --readFilesCommand gunzip -c parameter to the above mapping command. STAR Parameters description for mapping reads to genome, Parameter Description--runThreadN: ealing hmo applicationWebApr 13, 2024 · The text was updated successfully, but these errors were encountered: ealing hockeyWebJul 6, 2024 · Hi @Gotumbtai. nothing suspicious in the Log.out file. It seems like the FASTQ files are already pre-sorted (generated from a sorted BAM?) file, which requires more RAM for sorting, but still should work fine. ealing hilton hotelWebNov 1, 2024 · readFilesCommand - Notes on how to process the read files (in this case use zcat to unzip them) readFilesIn - The forward and reverse reads; outSAMtype - Type of … c++ special characters in stringWebNov 17, 2024 · --readFilesCommand gunzip -cparameter to the above mapping command. STAR Parameters description for mapping reads to genome, If your study goal is to … ealing hmo licensingWebOct 16, 2024 · Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community. ealing hockey club