install command for hisat2 and sam tools in debian linux

Question

[miravet65]

i want install hisat2 and sam tools in linux . i dont know commands for install . are there links for download these tools thanks

Answer 1

[Devon Ryan]

hisat2 can be downloaded from the project's website. samtools can either be downloaded and compiled from the samtools website or you can install a slightly older version with apt-get install (the same command can be used to install most things on Debian).

Alternatively, install conda and conda install -c bioconda samtools hisat2.

[miravet65]

thanks for answer. i want use of hisat2 for one sample that is fastq format and pair end . i know command for hisat 2 but i dont for one sample replace input in command. my index is hg38 , sample is SRR178854_1 , SRR178854_2 and commands for hisat2 is hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <sra accession="" number="">} [-S <hit>] i dont know [options ] or -U . m1 , m2 and in the final i want a sam format file for two read. there is same problem for me in hteseq for one sample . can you help me . ? thanks

[Devon Ryan]

[options] are whatever options you want to give, see the documentation. {-1 <m1> -2 <m2> | -U <r> | --sra-acc <sra accession="" number="">} means that you should give one of the following: -1 and -2 for paired-end experiments; -U for single-end experiments; and --sra-acc for experiments from SRA. You have paired-end data, so give the files as appropriate with -1 and -2.

I highly recommend that you not continue doing this analysis yourself, especially from the command line. You don't have the requisite knowledge necessary to do this correctly and the learning curve when starting this on the command line is not worth your time. Go to a training session (likely with Galaxy, where you could do all of this without needing to deal with the underlying software) or find a collaborator.

[miravet65]

Thank you very much for a very worthwhile and useful tips I like to do myself.if there is not problem for you . can you send your E.mail for me . because i doing all of the step by linux and i know almost R program for analysis with Deseq2 , edgr2 just two steps are difficult for me (hisat2 , htseq count) because command in two step are problem for me and i dont know .but i doing trimming and quality check for samples and read .