Entering edit mode
6.5 years ago
Arindam Ghosh
▴
510
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
Thank you very much for the links and the suggestion.
I am using the Griffith lab protocol and it has proved to be very useful.
Please add link for griffith lab protocol
Informatics for RNA-seq: A web resource for analysis on the cloud
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 symbolmbedtls_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 2Would you please tell me how to fix this? Thank you so much!