Can anyone suggest a good tutorial to learn RNA-seq analysis?
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7.1 years ago
Arindam Ghosh ▴ 530

Can anyone suggest a good tutorial to learn RNA-seq data analysis? I am for the first time handling NGS data. Before I start with my own data I need some tutorials to learn about the technique.

[Updated 17 Aug 2022] My own RNA-seq step-by-step tutorial: Transcriptomic Analysis of Human Naïve and Primed Pluripotent Stem Cells

analysis RNA-Seq ngs • 29k views
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7.1 years ago
  • A nice paper here
  • A nice blog/tutorial here
  • And one more here

One last suggestion - understand the biology first! "Why" first, then "how".

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Thank you very much for the links and the suggestion.

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I am using the Griffith lab protocol and it has proved to be very useful.

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Please add link for griffith lab protocol

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Thank you for sharing! Where can I post questions about GitHub page of Griffith lab?
I run this code

cd $RNA_HOME/student_tools/ export SAMTOOLS_ROOT=$RNA_HOME/student_tools/samtools-1.9 git clone https://github.com/genome/bam-readcount.git cd bam-readcount cmake -Wno-dev $RNA_HOME/student_tools/bam-readcount make

After a quite long-running, I got error:

[ 11%] Built target boost-1.55 [ 11%] Built target __bc_predepends [ 22%] Built target bzip2 [ 33%] Built target mbedtls [ 34%] Performing build step for 'curl' Making all in lib CCLD libcurl.la /usr/bin/ld: /vcu_gpfs2/home/doanc2/workspace/rnaseq/student_tools/bam-readcount/vendor/mbedtls/lib/libmbedtls.a(ssl_ciphersuites.o): relocation R_X86_64_32 against .bss' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /vcu_gpfs2/home/doanc2/workspace/rnaseq/student_tools/bam-readcount/vendor/mbedtls/lib/libmbedtls.a(ssl_tls.o): relocation R_X86_64_32 against.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /vcu_gpfs2/home/doanc2/workspace/rnaseq/student_tools/bam-readcount/vendor/mbedtls/lib/libmbedtls.a(debug.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /vcu_gpfs2/home/doanc2/workspace/rnaseq/student_tools/bam-readcount/vendor/mbedtls/lib/libmbedtls.a(ssl_cli.o): relocation R_X86_64_32 against.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /vcu_gpfs2/home/doanc2/workspace/rnaseq/student_tools/bam-readcount/vendor/mbedtls/lib/libmbedtls.a(ssl_srv.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /vcu_gpfs2/home/doanc2/workspace/rnaseq/student_tools/bam-readcount/vendor/mbedtls/lib/libmbedx509.a(x509_crl.o): relocation R_X86_64_32 against.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /vcu_gpfs2/home/doanc2/workspace/rnaseq/student_tools/bam-readcount/vendor/mbedtls/lib/libmbedx509.a(x509_crt.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /vcu_gpfs2/home/doanc2/workspace/rnaseq/student_tools/bam-readcount/vendor/mbedtls/lib/libmbedx509.a(x509.o): relocation R_X86_64_32 against.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /vcu_gpfs2/home/doanc2/workspace/rnaseq/student_tools/bam-readcount/vendor/mbedtls/lib/libmbedcrypto.a(bignum.o): relocation R_X86_64_32S against .rodata.str1.1' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /vcu_gpfs2/home/doanc2/workspace/rnaseq/student_tools/bam-readcount/vendor/mbedtls/lib/libmbedcrypto.a(cipher.o): relocation R_X86_64_32 against undefined symbolmbedtls_cipher_supported' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /vcu_gpfs2/home/doanc2/workspace/rnaseq/student_tools/bam-readcount/vendor/mbedtls/lib/libmbedcrypto.a(ctr_drbg.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /vcu_gpfs2/home/doanc2/workspace/rnaseq/student_tools/bam-readcount/vendor/mbedtls/lib/libmbedcrypto.a(des.o): relocation R_X86_64_32S against.rodata' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /vcu_gpfs2/home/doanc2/workspace/rnaseq/student_tools/bam-readcount/vendor/mbedtls/lib/libmbedcrypto.a(dhm.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /vcu_gpfs2/home/doanc2/workspace/rnaseq/student_tools/bam-readcount/vendor/mbedtls/lib/libmbedcrypto.a(ecp.o): relocation R_X86_64_32 against.rodata' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /vcu_gpfs2/home/doanc2/workspace/rnaseq/student_tools/bam-readcount/vendor/mbedtls/lib/libmbedcrypto.a(ecp_curves.o): relocation R_X86_64_32S against .data' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /vcu_gpfs2/home/doanc2/workspace/rnaseq/student_tools/bam-readcount/vendor/mbedtls/lib/libmbedcrypto.a(entropy.o): relocation R_X86_64_32S against symbolmbedtls_platform_entropy_poll' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /vcu_gpfs2/home/doanc2/workspace/rnaseq/student_tools/bam-readcount/vendor/mbedtls/lib/libmbedcrypto.a(entropy_poll.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /vcu_gpfs2/home/doanc2/workspace/rnaseq/student_tools/bam-readcount/vendor/mbedtls/lib/libmbedcrypto.a(error.o): relocation R_X86_64_32 against.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /vcu_gpfs2/home/doanc2/workspace/rnaseq/student_tools/bam-readcount/vendor/mbedtls/lib/libmbedcrypto.a(gcm.o): relocation R_X86_64_32S against .rodata' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /vcu_gpfs2/home/doanc2/workspace/rnaseq/student_tools/bam-readcount/vendor/mbedtls/lib/libmbedcrypto.a(md.o): relocation R_X86_64_32 against.rodata' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /vcu_gpfs2/home/doanc2/workspace/rnaseq/student_tools/bam-readcount/vendor/mbedtls/lib/libmbedcrypto.a(md5.o): relocation R_X86_64_32 against .rodata' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /vcu_gpfs2/home/doanc2/workspace/rnaseq/student_tools/bam-readcount/vendor/mbedtls/lib/libmbedcrypto.a(oid.o): relocation R_X86_64_32 against.rodata' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /vcu_gpfs2/home/doanc2/workspace/rnaseq/student_tools/bam-readcount/vendor/mbedtls/lib/libmbedcrypto.a(pem.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /vcu_gpfs2/home/doanc2/workspace/rnaseq/student_tools/bam-readcount/vendor/mbedtls/lib/libmbedcrypto.a(pk.o): relocation R_X86_64_32S against.rodata' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /vcu_gpfs2/home/doanc2/workspace/rnaseq/student_tools/bam-readcount/vendor/mbedtls/lib/libmbedcrypto.a(pk_wrap.o): relocation R_X86_64_32S against .rodata.str1.1' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /vcu_gpfs2/home/doanc2/workspace/rnaseq/student_tools/bam-readcount/vendor/mbedtls/lib/libmbedcrypto.a(pkparse.o): relocation R_X86_64_32 against.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /vcu_gpfs2/home/doanc2/workspace/rnaseq/student_tools/bam-readcount/vendor/mbedtls/lib/libmbedcrypto.a(pkwrite.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /vcu_gpfs2/home/doanc2/workspace/rnaseq/student_tools/bam-readcount/vendor/mbedtls/lib/libmbedcrypto.a(ripemd160.o): relocation R_X86_64_32 against.rodata' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /vcu_gpfs2/home/doanc2/workspace/rnaseq/student_tools/bam-readcount/vendor/mbedtls/lib/libmbedcrypto.a(rsa.o): relocation R_X86_64_32 against .rodata.str1.8' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /vcu_gpfs2/home/doanc2/workspace/rnaseq/student_tools/bam-readcount/vendor/mbedtls/lib/libmbedcrypto.a(sha1.o): relocation R_X86_64_32 against.rodata' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /vcu_gpfs2/home/doanc2/workspace/rnaseq/student_tools/bam-readcount/vendor/mbedtls/lib/libmbedcrypto.a(sha256.o): relocation R_X86_64_32 against .rodata' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /vcu_gpfs2/home/doanc2/workspace/rnaseq/student_tools/bam-readcount/vendor/mbedtls/lib/libmbedcrypto.a(sha512.o): relocation R_X86_64_32 against.rodata' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /vcu_gpfs2/home/doanc2/workspace/rnaseq/student_tools/bam-readcount/vendor/mbedtls/lib/libmbedcrypto.a(aes.o): relocation R_X86_64_32 against .bss' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /vcu_gpfs2/home/doanc2/workspace/rnaseq/student_tools/bam-readcount/vendor/mbedtls/lib/libmbedcrypto.a(arc4.o): relocation R_X86_64_32 against.rodata' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /vcu_gpfs2/home/doanc2/workspace/rnaseq/student_tools/bam-readcount/vendor/mbedtls/lib/libmbedcrypto.a(ecdsa.o): relocation R_X86_64_32S against symbol mbedtls_hmac_drbg_random' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /vcu_gpfs2/home/doanc2/workspace/rnaseq/student_tools/bam-readcount/vendor/mbedtls/lib/libmbedcrypto.a(pkcs5.o): relocation R_X86_64_32 against.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /vcu_gpfs2/home/doanc2/workspace/rnaseq/student_tools/bam-readcount/vendor/mbedtls/lib/libmbedcrypto.a(poly1305.o): relocation R_X86_64_32 against `.rodata' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: final link failed: Nonrepresentable section on output collect2: error: ld returned 1 exit status make[5]: [libcurl.la] Error 1 make[4]: [all] Error 2 make[3]: [all-recursive] Error 1 make[2]: [vendor/src/curl-stamp/curl-build] Error 2 make[1]: [CMakeFiles/curl.dir/all] Error 2 make: [all] Error 2

Would you please tell me how to fix this? Thank you so much!

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7.1 years ago

Hello,

You can follow the blog "RNAseq Blog", an informative blog to start with "RNAseq data analysis". This blog is active on twitter too. I find this blog really helpful.

http://www.rna-seqblog.com/

Hope this helps.

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Yes, their articles are helping me a lot. Thank you.

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7.1 years ago

Hi Here are some good workflows Deseq2 , STHDA Hope it helps

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